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Sample records for all-atom force field

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  3. Nonequilibrium forces between atoms and dielectrics mediated by a quantum field

    International Nuclear Information System (INIS)

    Behunin, Ryan O.; Hu, Bei-Lok

    2011-01-01

    In this paper we give a first principles microphysics derivation of the nonequilibrium forces between an atom, treated as a three-dimensional harmonic oscillator, and a bulk dielectric medium modeled as a continuous lattice of oscillators coupled to a reservoir. We assume no direct interaction between the atom and the medium but there exist mutual influences transmitted via a common electromagnetic field. By employing concepts and techniques of open quantum systems we introduce coarse-graining to the physical variables--the medium, the quantum field, and the atom's internal degrees of freedom, in that order--to extract their averaged effects from the lowest tier progressively to the top tier. The first tier of coarse-graining provides the averaged effect of the medium upon the field, quantified by a complex permittivity (in the frequency domain) describing the response of the dielectric to the field in addition to its back action on the field through a stochastic forcing term. The last tier of coarse-graining over the atom's internal degrees of freedom results in an equation of motion for the atom's center of mass from which we can derive the force on the atom. Our nonequilibrium formulation provides a fully dynamical description of the atom's motion including back-action effects from all other relevant variables concerned. In the long-time limit we recover the known results for the atom-dielectric force when the combined system is in equilibrium or in a nonequilibrium stationary state.

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

    Science.gov (United States)

    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

  5. Nonequilibrium forces between neutral atoms mediated by a quantum field

    International Nuclear Information System (INIS)

    Behunin, Ryan O.; Hu, Bei-Lok

    2010-01-01

    We study forces between two neutral atoms, modeled as three-dimensional harmonic oscillators, arising from mutual influences mediated by an electromagnetic field but not from their direct interactions. We allow as dynamical variables the center-of-mass motion of the atom, its internal degrees of freedom, and the quantum field treated relativistically. We adopt the method of nonequilibrium quantum field theory which can provide a first-principles, systematic, and unified description including the intrinsic and induced dipole fluctuations. The inclusion of self-consistent back-actions makes possible a fully dynamical description of these forces valid for general atom motion. In thermal equilibrium we recover the known forces--London, van der Waals, and Casimir-Polder--between neutral atoms in the long-time limit. We also reproduce a recently reported force between atoms when the system is out of thermal equilibrium at late times. More noteworthy is the discovery of the existence of a type of (or identification of the source of some known) interatomic force which we call the ''entanglement force,'' originating from the quantum correlations of the internal degrees of freedom of entangled atoms.

  6. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

    International Nuclear Information System (INIS)

    Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

    2016-01-01

    An empirically parameterized intermolecular force field is developed for crystal structure modelling and prediction. The model is optimized for use with an atomic multipole description of electrostatic interactions. We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%

  7. A new united atom force field for adsorption of alkenes in zeolites

    NARCIS (Netherlands)

    Liu, B.; Smit, B.; Rey, F.; Valencia, S.; Calero, S.

    2008-01-01

    A new united atom force field was developed that accurately describes the adsorption properties of linear alkenes in zeolites. The force field was specifically designed for use in the inhomogeneous system and therefore a truncated and shifted potential was used. With the determined force field, we

  8. Refined OPLS All-Atom Force Field for Saturated Phosphatidylcholine Bilayers at Full Hydration

    DEFF Research Database (Denmark)

    Maciejewski, A.; Pasenkiewicz-Gierula, M.; Cramariuc, O.

    2014-01-01

    validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule....... In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Moller-Plesset perturbation theory (MP2), and (3...... one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM)....

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

    Science.gov (United States)

    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/ .

  10. Dipole and quadrupole forces exerted on atoms in laser fields: The nonperturbative approach

    International Nuclear Information System (INIS)

    Sindelka, Milan; Moiseyev, Nimrod; Cederbaum, Lorenz S.

    2006-01-01

    Manipulation of cold atoms by lasers has so far been studied solely within the framework of the conventional dipole approximation, and the atom-light interaction has been treated using low order perturbation theory. Laser control of atomic motions has been ascribed exclusively to the corresponding light-induced dipole forces. In this work, we present a general theory to derive the potential experienced by an atom in a monochromatic laser field in a context analogous to the Born-Oppenheimer approximation for molecules in the field-free case. The formulation goes beyond the dipole approximation and gives rise to the field-atom coupling potential terms which so far have not been taken into consideration in theoretical or experimental studies. Contrary to conventional approaches, our method is based upon the many electron Floquet theory and remains valid also for high intensity laser fields (i.e., for a strongly nonperturbative atom-light interaction). As an illustration of the developed theory, we investigate the trapping of cold atoms in optical lattices. We find that for some atoms for specific laser parameters, despite the absence of the dipole force, the laser trapping is still possible due to the electric quadrupole forces. Namely, we show that by using realistic laser parameters one can form a quadrupole optical lattice which is sufficiently strong to trap Ca and Na atoms

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

    Science.gov (United States)

    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.

  12. Atomic force microscopy. A new method for atom identification and manipulation

    International Nuclear Information System (INIS)

    Abe, Masayuki; Sugimoto, Yoshiaki; Morita, Seizo

    2007-01-01

    Frequency modulation atomic force microscopy (FM-AFM) is a scanning probe technique that detects the interaction forces between the outermost atom of a sharp tip and the atoms at a surface to image the sample surface. It is expected that the FM-AFM can cover the research field which scanning tunneling microscopy does not provide. In this article, we would introduce FM-AFM experiments applied to site-specific force measurements and atom manipulation, including how to solve the problems to achieve precise FM-AFM measurements. (author)

  13. Probing Field Distributions on Waveguide Structures with an Atomic Force/Photon Scanning Tunneling Microscope

    NARCIS (Netherlands)

    Borgonjen, E.G.; Borgonjen, E.G.; Moers, M.H.P.; Moers, M.H.P.; Ruiter, A.G.T.; van Hulst, N.F.

    1995-01-01

    A 'stand-alone' Photon Scanning Tunneling Microscope combined with an Atomic force Microscope, using a micro-fabricated silicon-nitride probe, is applied to the imaging of field distribution in integrated optical ridge waveguides. The electric field on the waveguide is locally probed by coupling to

  14. Examining the origins of the hydration force between lipid bilayers using all-atom simulations.

    Science.gov (United States)

    Gentilcore, Anastasia N; Michaud-Agrawal, Naveen; Crozier, Paul S; Stevens, Mark J; Woolf, Thomas B

    2010-05-01

    Using 237 all-atom double bilayer simulations, we examined the thermodynamic and structural changes that occur as a phosphatidylcholine lipid bilayer stack is dehydrated. The simulated system represents a micropatch of lipid multilayer systems that are studied experimentally using surface force apparatus, atomic force microscopy and osmotic pressure studies. In these experiments, the hydration level of the system is varied, changing the separation between the bilayers, in order to understand the forces that the bilayers feel as they are brought together. These studies have found a curious, strongly repulsive force when the bilayers are very close to each other, which has been termed the "hydration force," though the origins of this force are not clearly understood. We computationally reproduce this repulsive, relatively free energy change as bilayers come together and make qualitative conclusions as to the enthalpic and entropic origins of the free energy change. This analysis is supported by data showing structural changes in the waters, lipids and salts that have also been seen in experimental work. Increases in solvent ordering as the bilayers are dehydrated are found to be essential in causing the repulsion as the bilayers come together.

  15. All-Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model

    Science.gov (United States)

    Savelyev, Alexey; MacKerell, Alexander D.

    2014-01-01

    Presented is a first generation atomistic force field for DNA in which electronic polarization is modeled based on the classical Drude oscillator formalism. The DNA model is based on parameters for small molecules representative of nucleic acids, including alkanes, ethers, dimethylphosphate, and the nucleic acid bases and empirical adjustment of key dihedral parameters associated with the phosphodiester backbone, glycosidic linkages and sugar moiety of DNA. Our optimization strategy is based on achieving a compromise between satisfying the properties of the underlying model compounds in the gas phase targeting QM data and reproducing a number of experimental properties of DNA duplexes in the condensed phase. The resulting Drude force field yields stable DNA duplexes on the 100 ns time scale and satisfactorily reproduces (1) the equilibrium between A and B forms of DNA and (2) transitions between the BI and BII sub-states of B form DNA. Consistency with the gas phase QM data for the model compounds is significantly better for the Drude model as compared to the CHARMM36 additive force field, which is suggested to be due to the improved response of the model to changes in the environment associated with the explicit inclusion of polarizability. Analysis of dipole moments associated with the nucleic acid bases shows the Drude model to have significantly larger values than those present in CHARMM36, with the dipoles of individual bases undergoing significant variations during the MD simulations. Additionally, the dipole moment of water was observed to be perturbed in the grooves of DNA. PMID:24752978

  16. Atomic force and scanning near-field optical microscopy study of carbocyanine dye J-aggregates

    Czech Academy of Sciences Publication Activity Database

    Prokhorov, V.V.; Petrova, M.G.; Kovaleva, Natalia; Demikhov, E.I.

    2014-01-01

    Roč. 10, č. 5 (2014), s. 700-704 ISSN 1573-4137 Institutional support: RVO:68378271 Keywords : carbocyanine dye * elementary fibri * high-resolution atomic force microscopy * J-aggregate * probe microscopy * scanning near-field optical microscopy Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.096, year: 2014

  17. Resonance oscillations of nonreciprocal long-range van der Waals forces between atoms in electromagnetic fields

    Science.gov (United States)

    Sherkunov, Yury

    2018-03-01

    We study theoretically the van der Waals interaction between two atoms out of equilibrium with an isotropic electromagnetic field. We demonstrate that at large interatomic separations, the van der Waals forces are resonant, spatially oscillating, and nonreciprocal due to resonance absorption and emission of virtual photons. We suggest that the van der Waals forces can be controlled and manipulated by tuning the spectrum of artificially created random light.

  18. Survey on result promotion of the atomic force technique

    Energy Technology Data Exchange (ETDEWEB)

    Eguchi, Masato; Okuno, Yumiko [Nikkei Research Inst. of Industry and Markets, Tokyo (Japan)

    1998-02-01

    By change of environment around research and development of atomic force, investigation has been recently executed not only on a theme directing a specific aim, but also on technical development considering some applications to the other field reflected by social needs. Therefore, an effective procedure and program capable of reflecting and promoting results of the atomic fore development to other industrial field were necessary. In this study, methods of evaluation and industrialization on study results of the atomic force were investigated. As a result, in order to promote the study results to other field, it was found to be important that some free reasons and concept engineering to mediate between developing and applying sides were to be present. In addition, it was suggested by some searches that a new atomic industry has a probability to be created by using potential energies such as heat, radiation, pulse, and so on. In this paper, evaluation on industrialization of the atomic force technical resources, and establishment of the industrialization program were described. (G.K.)

  19. All-atom force field for molecular dynamics simulations on organotransition metal solids and liquids. Application to M(CO)(n) (M = Cr, Fe, Ni, Mo, Ru, or W) compounds.

    Science.gov (United States)

    Bernardes, Carlos E S; Canongia Lopes, José N; Minas da Piedade, Manuel E

    2013-10-31

    A previously developed OPLS-based all-atom force field for organometallic compounds was extended to a series of first-, second-, and third-row transition metals based on the study of M(CO)(n) (M = Cr, Fe, Ni, Mo, Ru, or W) complexes. For materials that are solid at ambient temperature and pressure (M = Cr, Mo, W) the validation of the force field was based on reported structural data and on the standard molar enthalpies of sublimation at 298.15 K, experimentally determined by Calvet-drop microcalorimetry using samples corresponding to a specific and well-characterized crystalline phase: Δ(sub)H(m)° = 72.6 ± 0.3 kJ·mol(–1) for Cr(CO)(6), 73.4 ± 0.3 kJ·mol(–1) for Mo(CO)(6), and 77.8 ± 0.3 kJ·mol(–1) for W(CO)(6). For liquids, where problems of polymorphism or phase mixtures are absent, critically analyzed literature data were used. The force field was able to reproduce the volumetric properties of the test set (density and unit cell volume) with an average deviations smaller than 2% and the experimentally determined enthalpies of sublimation and vaporization with an accuracy better than 2.3 kJ·mol(–1). The Lennard-Jones (12-6) potential function parameters used to calculate the repulsive and dispersion contributions of the metals within the framework of the force field were found to be transferable between chromium, iron, and nickel (first row) and between molybdenum and ruthenium (second row).

  20. Near field plasmon and force microscopy

    NARCIS (Netherlands)

    de Hollander, R.B.G.; van Hulst, N.F.; Kooyman, R.P.H.

    1995-01-01

    A scanning plasmon near field optical microscope (SPNM) is presented which combines a conventional far field surface plasmon microscope with a stand-alone atomic force microscope (AFM). Near field plasmon and force images are recorded simultaneously both with a lateral resolution limited by the

  1. Controlling Casimir force via coherent driving field

    Science.gov (United States)

    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.

  2. Light-induced gauge fields for ultracold atoms

    Science.gov (United States)

    Goldman, N.; Juzeliūnas, G.; Öhberg, P.; Spielman, I. B.

    2014-12-01

    Gauge fields are central in our modern understanding of physics at all scales. At the highest energy scales known, the microscopic universe is governed by particles interacting with each other through the exchange of gauge bosons. At the largest length scales, our Universe is ruled by gravity, whose gauge structure suggests the existence of a particle—the graviton—that mediates the gravitational force. At the mesoscopic scale, solid-state systems are subjected to gauge fields of different nature: materials can be immersed in external electromagnetic fields, but they can also feature emerging gauge fields in their low-energy description. In this review, we focus on another kind of gauge field: those engineered in systems of ultracold neutral atoms. In these setups, atoms are suitably coupled to laser fields that generate effective gauge potentials in their description. Neutral atoms ‘feeling’ laser-induced gauge potentials can potentially mimic the behavior of an electron gas subjected to a magnetic field, but also, the interaction of elementary particles with non-Abelian gauge fields. Here, we review different realized and proposed techniques for creating gauge potentials—both Abelian and non-Abelian—in atomic systems and discuss their implication in the context of quantum simulation. While most of these setups concern the realization of background and classical gauge potentials, we conclude with more exotic proposals where these synthetic fields might be made dynamical, in view of simulating interacting gauge theories with cold atoms.

  3. Light-induced gauge fields for ultracold atoms

    International Nuclear Information System (INIS)

    Goldman, N; Juzeliūnas, G; Öhberg, P; Spielman, I B

    2014-01-01

    Gauge fields are central in our modern understanding of physics at all scales. At the highest energy scales known, the microscopic universe is governed by particles interacting with each other through the exchange of gauge bosons. At the largest length scales, our Universe is ruled by gravity, whose gauge structure suggests the existence of a particle—the graviton—that mediates the gravitational force. At the mesoscopic scale, solid-state systems are subjected to gauge fields of different nature: materials can be immersed in external electromagnetic fields, but they can also feature emerging gauge fields in their low-energy description. In this review, we focus on another kind of gauge field: those engineered in systems of ultracold neutral atoms. In these setups, atoms are suitably coupled to laser fields that generate effective gauge potentials in their description. Neutral atoms ‘feeling’ laser-induced gauge potentials can potentially mimic the behavior of an electron gas subjected to a magnetic field, but also, the interaction of elementary particles with non-Abelian gauge fields. Here, we review different realized and proposed techniques for creating gauge potentials—both Abelian and non-Abelian—in atomic systems and discuss their implication in the context of quantum simulation. While most of these setups concern the realization of background and classical gauge potentials, we conclude with more exotic proposals where these synthetic fields might be made dynamical, in view of simulating interacting gauge theories with cold atoms. (review article)

  4. Evaluating amber force fields using computed NMR chemical shifts.

    Science.gov (United States)

    Koes, David R; Vries, John K

    2017-10-01

    NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical shifts generated from ab initio quantum calculations. This approach has potential utility for evaluating the force fields that underlie these simulations. Imperfections in force fields generate flawed atomic coordinates. Chemical shifts obtained from flawed coordinates have errors that can be traced back to these imperfections. We use this approach to evaluate a series of AMBER force fields that have been refined over the course of two decades (ff94, ff96, ff99SB, ff14SB, ff14ipq, and ff15ipq). For each force field a series of MD simulations are carried out for eight model proteins. The calculated chemical shifts for the 1 H, 15 N, and 13 C a atoms are compared with experimental values. Initial evaluations are based on root mean squared (RMS) errors at the protein level. These results are further refined based on secondary structure and the types of atoms involved in nonbonded interactions. The best chemical shift for identifying force field differences is the shift associated with peptide protons. Examination of the model proteins on a residue by residue basis reveals that force field performance is highly dependent on residue position. Examination of the time course of nonbonded interactions at these sites provides explanations for chemical shift differences at the atomic coordinate level. Results show that the newer ff14ipq and ff15ipq force fields developed with the implicitly polarized charge method perform better than the older force fields. © 2017 Wiley Periodicals, Inc.

  5. Interfacial force measurements using atomic force microscopy

    NARCIS (Netherlands)

    Chu, L.

    2018-01-01

    Atomic Force Microscopy (AFM) can not only image the topography of surfaces at atomic resolution, but can also measure accurately the different interaction forces, like repulsive, adhesive and lateral existing between an AFM tip and the sample surface. Based on AFM, various extended techniques have

  6. Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein

    Directory of Open Access Journals (Sweden)

    Raiker Witter

    2015-01-01

    Full Text Available Polarization of atoms plays a substantial role in molecular interactions. Class I and II force fields mostly calculate with fixed atomic charges which can cause inadequate descriptions for highly charged molecules, for example, ion channels or metalloproteins. Changes in charge distributions can be included into molecular mechanics calculations by various methods. Here, we present a very fast computational quantum mechanical method, the Bond Polarization Theory (BPT. Atomic charges are obtained via a charge calculation method that depend on the 3D structure of the system in a similar way as atomic charges of ab initio calculations. Different methods of population analysis and charge calculation methods and their dependence on the basis set were investigated. A refined parameterization yielded excellent correlation of R=0.9967. The method was implemented in the force field COSMOS-NMR and applied to the histidine-tryptophan-complex of the transmembrane domain of the M2 protein channel of influenza A virus. Our calculations show that moderate changes of side chain torsion angle χ1 and small variations of χ2 of Trp-41 are necessary to switch from the inactivated into the activated state; and a rough two-side jump model of His-37 is supported for proton gating in accordance with a flipping mechanism.

  7. Harmonic force field for nitro compounds.

    Science.gov (United States)

    Bellido, Edson P; Seminario, Jorge M

    2012-06-01

    Molecular simulations leading to sensors for the detection of explosive compounds require force field parameters that can reproduce the mechanical and vibrational properties of energetic materials. We developed precise harmonic force fields for alanine polypeptides and glycine oligopeptides using the FUERZA procedure that uses the Hessian tensor (obtained from ab initio calculations) to calculate precise parameters. In this work, we used the same procedure to calculate generalized force field parameters of several nitro compounds. We found a linear relationship between force constant and bond distance. The average angle in the nitro compounds was 116°, excluding the 90° angle of the carbon atoms in the octanitrocubane. The calculated parameters permitted the accurate molecular modeling of nitro compounds containing many functional groups. Results were acceptable when compared with others obtained using methods that are specific for one type of molecule, and much better than others obtained using methods that are too general (these ignore the chemical effects of surrounding atoms on the bonding and therefore the bond strength, which affects the mechanical and vibrational properties of the whole molecule).

  8. Near field plasmon and force microscopy

    OpenAIRE

    de Hollander, R.B.G.; van Hulst, N.F.; Kooyman, R.P.H.

    1995-01-01

    A scanning plasmon near field optical microscope (SPNM) is presented which combines a conventional far field surface plasmon microscope with a stand-alone atomic force microscope (AFM). Near field plasmon and force images are recorded simultaneously both with a lateral resolution limited by the probe size to about 20 nm. At variance to previous work, utilizing a scanning tunneling microscope (STM) with a metallic tip, a dielectric silicon-nitride tip is used in contact mode. This arrangement ...

  9. Dynamics of moving interacting atoms in a laser radiation field and optical size resonances

    International Nuclear Information System (INIS)

    Gadomskii, O.N.; Glukhov, A.G.

    2005-01-01

    The forces acting on interacting moving atoms exposed to resonant laser radiation are calculated. It is shown that the forces acting on the atoms include the radiation pressure forces as well as the external and internal bias forces. The dependences of the forces on the atomic spacing, polarization, and laser radiation frequency are given. It is found that the internal bias force associated with the interaction of atomic dipoles via the reemitted field may play an important role in the dynamics of dense atomic ensembles in a light field. It is shown that optical size resonances appear in the system of interacting atoms at frequencies differing substantially from transition frequencies in the spectrum of atoms. It is noted that optical size resonances as well as the Doppler frequency shift in the spectrum of interacting atoms play a significant role in the processes of laser-radiation-controlled motion of the atoms

  10. Communication: Multiple atomistic force fields in a single enhanced sampling simulation

    Energy Technology Data Exchange (ETDEWEB)

    Hoang Viet, Man [Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202 (United States); Derreumaux, Philippe, E-mail: philippe.derreumaux@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France); Institut Universitaire de France, 103 Bvd Saint-Germain, 75005 Paris (France); Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)

    2015-07-14

    The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water.

  11. Using atom interferometry to search for new forces

    International Nuclear Information System (INIS)

    Wacker, Jay G.

    2010-01-01

    Atom interferometry is a rapidly advancing field and this Letter proposes an experiment based on existing technology that can search for new short distance forces. With current technology it is possible to improve the sensitivity by up to a factor of 10 2 and near-future advances may be able to rewrite the limits for forces with ranges from 1 mm to 100 m.

  12. Using Atom Interferometry to Search for New Forces

    International Nuclear Information System (INIS)

    Wacker, Jay G.

    2009-01-01

    Atom interferometry is a rapidly advancing field and this Letter proposes an experiment based on existing technology that can search for new short distance forces. With current technology it is possible to improve the sensitivity by up to a factor of 10 2 and near-future advances will be able to rewrite the limits for forces with ranges from 100 (micro)m to 1km.

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

    OpenAIRE

    Savelyev, Alexey; MacKerell, Alexander D.

    2014-01-01

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

  14. Atomic motion in a high-intensity standing wave laser field

    International Nuclear Information System (INIS)

    Saez Ramdohr, L.F.

    1987-01-01

    This work discusses the effect of a high-intensity standing wave laser field on the motion of neutral atoms moving with a relatively high velocity. The analysis involves a detailed calculation of the force acting on the atoms and the calculation of the diffusion tensor associated with the fluctuations of the quantum force operator. The high-intensity laser field limit corresponds to a Rabi frequency much greater than the natural rate of the atom. The general results are valid for any atomic velocity. Results are then specialized to the case of slow and fast atoms where the Doppler shift of the laser frequency due to the atomic motion is either smaller or larger than the natural decay rate of the atom. The results obtained for the force and diffusion tensor are applied to a particular ideal experiment that studies the evolution of a fast atomic beam crossing a high-intensity laser beam. The theories developed previously, for a similar laser configuration, discuss only the low atomic velocities case and not the more realistic case of fast atoms. Here, an approximate solution of the equation for the distribution is obtained. Starting from the approximate distribution function, the deflection angle and dispersion angle for the atomic beam with respect to the free motion are calculated

  15. Taking nanomedicine teaching into practice with atomic force microscopy and force spectroscopy.

    Science.gov (United States)

    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.

  16. Casimir-Polder forces on atoms in the presence of magnetoelectronic bodies

    International Nuclear Information System (INIS)

    Buhmann, S.Y.

    2007-01-01

    In this work, the CP force between a single neutral atom or molecule and neutral magnetoelectric bodies is studied. The focus lies on the pure vacuum CP force, i.e., the electromagnetic field is in general understood to be in its ground state. Furthermore, we assume that the atom-body separation is sufficiently large to ensure that the atom is adequately characterised as an electric dipole, while the body can be described by its macroscopic magnetoelectric properties; and that repulsive exchange forces due to the overlap between the electronic wave functions of the atom and the bodies can be neglected. Interactions due to non-vanishing net charges, permanent electric dipole moments, magnetisability, quadrupole (or higher multipole) polarisabilities of the atom and those resulting from non-local or anisotropic magnetoelectric properties of the bodies are ignored. (orig.)

  17. Casimir-Polder forces on atoms in the presence of magnetoelectronic bodies

    Energy Technology Data Exchange (ETDEWEB)

    Buhmann, S Y

    2007-07-05

    In this work, the CP force between a single neutral atom or molecule and neutral magnetoelectric bodies is studied. The focus lies on the pure vacuum CP force, i.e., the electromagnetic field is in general understood to be in its ground state. Furthermore, we assume that the atom-body separation is sufficiently large to ensure that the atom is adequately characterised as an electric dipole, while the body can be described by its macroscopic magnetoelectric properties; and that repulsive exchange forces due to the overlap between the electronic wave functions of the atom and the bodies can be neglected. Interactions due to non-vanishing net charges, permanent electric dipole moments, magnetisability, quadrupole (or higher multipole) polarisabilities of the atom and those resulting from non-local or anisotropic magnetoelectric properties of the bodies are ignored. (orig.)

  18. Atomic force and optical near-field microscopic investigations of polarization holographic gratings in a liquid crystalline azobenzene side-chain polyester

    DEFF Research Database (Denmark)

    Ramanujam, P.S.; Holme, N.C.R.; Hvilsted, S.

    1996-01-01

    Atomic force and scanning near-field optical microscopic investigations have been carried out on a polarization holographic grating recorded in an azobenzene side-chain Liquid crystalline polyester. It has been found that immediately following laser irradiation, a topographic surface grating...

  19. Magnetic moment measurement of magnetic nanoparticles using atomic force microscopy

    International Nuclear Information System (INIS)

    Park, J-W; Lee, E-C; Ju, H; Yoo, I S; Chang, W-S; Chung, B H; Kim, B S

    2008-01-01

    Magnetic moment per unit mass of magnetic nanoparticles was found by using the atomic force microscope (AFM). The mass of the nanoparticles was acquired from the resonance frequency shift of the particle-attached AFM probe and magnetic force measurement was also carried out with the AFM. Combining with magnetic field strength, the magnetic moment per unit mass of the nanoparticles was determined as a function of magnetic field strength. (technical design note)

  20. All-(111) surface silicon nanowire field effect transistor devices: Effects of surface preparations

    NARCIS (Netherlands)

    Masood, M.N.; Carlen, Edwin; van den Berg, Albert

    2014-01-01

    Etching/hydrogen termination of All-(111) surface silicon nanowire field effect (SiNW-FET) devices developed by conventional photolithography and plane dependent wet etchings is studied with X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), atomic force microscopy (AFM) and

  1. AtomicJ: An open source software for analysis of force curves

    Science.gov (United States)

    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.

  2. AtomicJ: An open source software for analysis of force curves

    International Nuclear Information System (INIS)

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

    2014-01-01

    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

  3. Development and application of a free energy force field for all atom protein folding

    International Nuclear Information System (INIS)

    Verma, A.

    2007-11-01

    Proteins are the workhorses of all cellular life. They constitute the building blocks and the machinery of all cells and typically function in specific three-dimensional conformations into which each protein folds. Currently over one million protein sequences are known, compared to about 40,000 structures deposited in the Protein Data Bank (the world-wide database of protein structures). Reliable theoretical methods for protein structure prediction could help to reduce the gap between sequence and structural databases and elucidate the biological information in structurally unresolved sequences. In this thesis we explore an approach for protein structure prediction and folding that is based on the Anfinsen's hypothesis that most proteins in their native state are in thermodynamic equilibrium with their environment. We have developed a free energy forcefield (PFF02) that locates the native conformation of many proteins from all structural classes at the global minimum of the free-energy model. We have validated the forcefield against a large decoy set (Rosetta). The average root mean square deviation (RMSD) for the lowest energy structure for the 32 proteins of the decoy set was only 2.14 Aa from the experimental conformation. We have successfully implemented and used stochastic optimization methods, such as the basin hopping technique and evolutionary algorithms for all atom protein structure prediction. The evolutionary algorithm performs exceptionally well on large supercomputational architectures, such as BlueGene and MareNostrum. Using the PFF02 forcefield, we were able to fold 13 proteins (12-56 amino acids), which include helix, sheet and mixed secondary structure. On average the predicted structure of these proteins deviated from their experimental conformation by only 2.89 Aa RMSD. (orig.)

  4. Small amplitude atomic force spectroscopy

    NARCIS (Netherlands)

    de Beer, Sissi; van den Ende, Henricus T.M.; Ebeling, Daniel; Mugele, Friedrich Gunther; Bhushan, Bharat

    2011-01-01

    Over the years atomic force microscopy has developed from a pure imaging technique to a tool that can be employed for measuring quantitative tip–sample interaction forces. In this chapter we provide an overview of various techniques to extract quantitative tip–sample forces focusing on both

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

    Science.gov (United States)

    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.

  6. Complete all-atom hydrodynamics of protein unfolding in uniform flow

    International Nuclear Information System (INIS)

    Wang, Guan M; Sandberg, William C

    2010-01-01

    The unfolding dynamics of a protein, ubiquitin, pinned in several uniform flows, was studied at low and high flow rates in an all-atom style through a non-equilibrium molecular dynamics approach with explicit water molecules included. Atomic hydrodynamic force components on individual amino acids, as a function of time, due to the collisional interactions with the flowing water molecules were calculated explicitly. The protein conformational change in response to those time-varying forces was computed completely at the high flow rate up to nanosecond until the fully stretched state was reached. The end-to-end length of the single ubiquitin protein molecule at high flow rate is smoothly increasing. The step-like jumps between metastable states that describe the μm ms -1 scale force pulling experiments conducted on polyubiquitins at low flow rates, are not seen at the high flow speeds necessary to computationally probe the ns nm -1 scale regime. No unfolding was observed in the low flow rate atomic computations at nanosecond scale while partial and complete unfolding was observed in the coarse-grained low flow rate computations at microsecond scale. Examination of the all-atom computation of the time variation of the hydrodynamic forces on, and the velocity components of, the protein molecule unveiled to some extent the details of the complexity of the hydrodynamic friction variation in the nm ns -1 regime of high rate flow-driven protein unfolding. This demonstrates quantitatively that all-atom computations are more suitable than the Langevin equation or Brownian dynamics methods for probing the interaction dynamics and resulting conformational dynamics of protein unfolding in strong flows on nm ns -1 time/length scales while the reverse is true for investigation of slow, diffusively driven systems.

  7. Novel parallel plate condenser for single particle electrostatic force measurements in atomic force microscope

    KAUST Repository

    Kwek, Jin Wang

    2011-07-01

    A combination of small parallel plate condenser with Indium Tin Oxide (ITO) glass slides as electrodes and an atomic force microscope (AFM) is used to characterize the electrostatic behavior of single glass bead microparticles (105-150 μm) glued to the AFM cantilever. This novel setup allows measurements of the electrostatic forces acting on a particle in an applied electrical field to be performed in ambient air conditions. By varying the position of the microparticle between the electrodes and the strength of the applied electric field, the relative contributions of the particle net charge, induced and image charges were investigated. When the microparticle is positioned in the middle of the electrodes, the force acting on the microparticle was linear with the applied electric field and proportional to the microparticle net charge. At distances close to the bottom electrode, the force follows a parabolic relationship with the applied electric field reflecting the contributions of induced and image charges. The method can be used for the rapid evaluation of the charging and polarizability properties of the microparticle as well as an alternative to the conventional Faraday\\'s pail technique. © 2011 Elsevier B.V.

  8. Force modulation for improved conductive-mode atomic force microscopy

    NARCIS (Netherlands)

    Koelmans, W.W.; Sebastian, Abu; Despont, Michel; Pozidis, Haris

    We present an improved conductive-mode atomic force microscopy (C-AFM) method by modulating the applied loading force on the tip. Unreliable electrical contact and tip wear are the primary challenges for electrical characterization at the nanometer scale. The experiments show that force modulation

  9. Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

    Science.gov (United States)

    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

  10. Minimizing tip-sample forces in jumping mode atomic force microscopy in liquid

    Energy Technology Data Exchange (ETDEWEB)

    Ortega-Esteban, A. [Departamento de Fisica de la Materia Condensada, C-3, Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain); Horcas, I. [Nanotec Electronica S.L., Centro Empresarial Euronova 3, Ronda de Poniente 12, 28760 Tres Cantos, Madrid (Spain); Hernando-Perez, M. [Departamento de Fisica de la Materia Condensada, C-3, Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain); Ares, P. [Nanotec Electronica S.L., Centro Empresarial Euronova 3, Ronda de Poniente 12, 28760 Tres Cantos, Madrid (Spain); Perez-Berna, A.J.; San Martin, C.; Carrascosa, J.L. [Centro Nacional de Biotecnologia (CNB-CSIC), Darwin 3, 28049 Madrid (Spain); Pablo, P.J. de [Departamento de Fisica de la Materia Condensada, C-3, Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain); Gomez-Herrero, J., E-mail: julio.gomez@uam.es [Departamento de Fisica de la Materia Condensada, C-3, Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain)

    2012-03-15

    Control and minimization of tip-sample interaction forces are imperative tasks to maximize the performance of atomic force microscopy. In particular, when imaging soft biological matter in liquids, the cantilever dragging force prevents identification of the tip-sample mechanical contact, resulting in deleterious interaction with the specimen. In this work we present an improved jumping mode procedure that allows detecting the tip-sample contact with high accuracy, thus minimizing the scanning forces ({approx}100 pN) during the approach cycles. To illustrate this method we report images of human adenovirus and T7 bacteriophage particles which are prone to uncontrolled modifications when using conventional jumping mode. -- Highlights: Black-Right-Pointing-Pointer Improvement in atomic force microscopy in buffer solution. Black-Right-Pointing-Pointer Peak force detection. Black-Right-Pointing-Pointer Subtracting the cantilever dragging force. Black-Right-Pointing-Pointer Forces in the 100 pN range. Black-Right-Pointing-Pointer Imaging of delicate viruses with atomic force microscopy.

  11. Observation of self-assembled fluorescent beads by scanning near-field optical microscopy and atomic force microscopy

    International Nuclear Information System (INIS)

    Oh, Y.J.; Jo, W.; Kim, Min-Gon; Kyu Park, Hyun; Hyun Chung, Bong

    2006-01-01

    Optical response and topography of fluorescent latex beads both on flat self-assembled monolayer and on a micron-patterned surface with poly(dimethylsiloxane) are studied. Scanning near-field optical microscopy and atomic force microscopy were utilized together for detecting fluorescence and imaging topography of the patterned latex beads, respectively. As a result, the micro-patterned latex beads where a specific chemical binding occurred show a strong signal, whereas no signals are observed in the case of nonspecific binding. With fluorescein isothiocyanate (FITC), it is convenient to measure fluorescence signal from the patterned beads allowing us to monitor the small balls of fluorescent latex

  12. Multifarious applications of atomic force microscopy in forensic science investigations.

    Science.gov (United States)

    Pandey, Gaurav; Tharmavaram, Maithri; Rawtani, Deepak; Kumar, Sumit; Agrawal, Y

    2017-04-01

    Forensic science is a wide field comprising of several subspecialties and uses methods derived from natural sciences for finding criminals and other evidence valid in a legal court. A relatively new area; Nano-forensics brings a new era of investigation in forensic science in which instantaneous results can be produced that determine various agents such as explosive gasses, biological agents and residues in different crime scenes and terrorist activity investigations. This can be achieved by applying Nanotechnology and its associated characterization techniques in forensic sciences. Several characterization techniques exist in Nanotechnology and nano-analysis is one such technique that is used in forensic science which includes Electron microscopes (EM) like Transmission (TEM) and Scanning (SEM), Raman microscopy (Micro -Raman) and Scanning Probe Microscopes (SPMs) like Atomic Force Microscope (AFM). Atomic force microscopy enables surface characterization of different materials by examining their morphology and mechanical properties. Materials that are immeasurable such as hair, body fluids, textile fibers, documents, polymers, pressure sensitive adhesives (PSAs), etc. are often encountered during forensic investigations. This review article will mainly focus on the use of AFM in the examination of different evidence such as blood stains, forged documents, human hair samples, ammunitions, explosives, and other such applications in the field of Forensic Science. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Atomic Force Microscope

    Energy Technology Data Exchange (ETDEWEB)

    Day, R.D.; Russell, P.E.

    1988-12-01

    The Atomic Force Microscope (AFM) is a recently developed instrument that has achieved atomic resolution imaging of both conducting and non- conducting surfaces. Because the AFM is in the early stages of development, and because of the difficulty of building the instrument, it is currently in use in fewer than ten laboratories worldwide. It promises to be a valuable tool for obtaining information about engineering surfaces and aiding the .study of precision fabrication processes. This paper gives an overview of AFM technology and presents plans to build an instrument designed to look at engineering surfaces.

  14. All-optical 3D atomic loops generated with Bessel light fields

    International Nuclear Information System (INIS)

    Volke-Sepulveda, Karen; Jauregui, RocIo

    2009-01-01

    The propagation invariance of Bessel beams as well as their transversal structure is used to perform a comparative analysis of their effect on cold atoms for four different configurations and combinations thereof. We show that, even at temperatures for which the classical description of the atom's centre-of-mass motion is valid, the interchange of momentum, energy and orbital angular momentum between light and atoms yields efficient tools for all-optical trapping, transporting and, in general, manipulating the state of motion of cold atoms.

  15. Self-consistent Optomechanical Dynamics and Radiation Forces in Thermal Light Fields

    International Nuclear Information System (INIS)

    Sonnleitner, M.

    2014-01-01

    We discuss two different aspects of the mechanical interaction between neutral matter and electromagnetic radiation.The first part addresses the complex dynamics of an elastic dielectric deformed by optical forces. To do so we use a one-dimensional model describing the medium by an array of beam splitters such that the interaction with the incident waves can be described with a transfer-matrix approach. Since the force on each individual beam splitter is known we thus obtain the correct volumetric force density inside the medium. Sending a light field through an initially homogeneous dielectric then results in density modulations which in turn alter the optical properties of this medium.The second part is concerned with mechanical light-effects on atoms in thermal radiation fields. At hand of a generic setup of an atom interacting with a hot sphere emitting blackbody radiation we show that the emerging gradient force may surpass gravity by several orders of magnitude. The strength of the repulsive scattering force strongly depends on the spectrum of the involved atoms and can be neglected in some setups. A special emphasis lies on possible implications on astrophysical scenarios where the interactions between heated dust and atoms, molecules or nanoparticles are of crucial interest. (author) [de

  16. Hydrogen atom moving across a magnetic field

    International Nuclear Information System (INIS)

    Lozovik, Yu.E.; Volkov, S.Yu.

    2004-01-01

    A hydrogen atom moving across a magnetic field is considered in a wide region of magnitudes of magnetic field and atom momentum. We solve the Schroedinger equation of the system numerically using an imaginary time method and find wave functions of the lowest states of atom. We calculate the energy and the mean electron-nucleus separation as a function of atom momentum and magnetic field. All the results obtained could be summarized as a phase diagram on the 'atom-momentum - magnetic-field' plane. There are transformations of wave-function structure at critical values of atom momentum and magnetic field that result in a specific behavior of dependencies of energy and mean interparticle separation on the atom momentum P. We discuss a transition from the Zeeman regime to the high magnetic field regime. A qualitative analysis of the complicated behavior of wave functions vs P based on the effective potential examination is given. We analyze a sharp transition at the critical momentum from a Coulomb-type state polarized due to atom motion to a strongly decentered (Landau-type) state at low magnetic fields. A crossover occurring at intermediate magnetic fields is also studied

  17. 4. All-Russian (international) scientific conference. Physicochemical processes during selection of atoms and molecules. Collection of reports

    International Nuclear Information System (INIS)

    Baranov, V.Yu.; Kolesnikov, Yu.A.

    1999-01-01

    The reports of the 4. All-Russian (international) scientific conference: Physicochemical processes during selection of atoms and molecules, are presented. The conference took place in Zvenigorod, 4-8 October, 1999. Contents of the reports are the following: laser isotope separation of molecules and atoms; isotopic selection of molecules and atoms in the field of centrifugal forces; selection of molecules by means of rectification and isotopic exchange methods; separation of isotopes by ion cyclotron-resonance method, in electric discharge and electromagnetic field; change in physical properties of substances which variation of their natural isotopic composition; use of isotopes in pharmacy preparation; status of experimental and diagnostic technique; certain promising methods of selection of atoms and molecules. The problems of laser separation of uranium isotopes, separation of carbon isotopes by multi-photon selective dissociation are discussed. The procedures permitting production of isotopes with high concentration and efficiency are developed [ru

  18. Multiloop atom interferometer measurements of chameleon dark energy in microgravity

    Science.gov (United States)

    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.

  19. Comparison of three empirical force fields for phonon calculations in CdSe quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Kelley, Anne Myers [Chemistry and Chemical Biology, University of California, Merced, 5200 North Lake Road, Merced, California 95343 (United States)

    2016-06-07

    Three empirical interatomic force fields are parametrized using structural, elastic, and phonon dispersion data for bulk CdSe and their predictions are then compared for the structures and phonons of CdSe quantum dots having average diameters of ~2.8 and ~5.2 nm (~410 and ~2630 atoms, respectively). The three force fields include one that contains only two-body interactions (Lennard-Jones plus Coulomb), a Tersoff-type force field that contains both two-body and three-body interactions but no Coulombic terms, and a Stillinger-Weber type force field that contains Coulombic interactions plus two-body and three-body terms. While all three force fields predict nearly identical peak frequencies for the strongly Raman-active “longitudinal optical” phonon in the quantum dots, the predictions for the width of the Raman peak, the peak frequency and width of the infrared absorption peak, and the degree of disorder in the structure are very different. The three force fields also give very different predictions for the variation in phonon frequency with radial position (core versus surface). The Stillinger-Weber plus Coulomb type force field gives the best overall agreement with available experimental data.

  20. Perspective: Ab initio force field methods derived from quantum mechanics

    Science.gov (United States)

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

    2018-03-01

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

  1. The Röntgen interaction and forces on dipoles in time-modulated optical fields

    Science.gov (United States)

    Sonnleitner, Matthias; Barnett, Stephen M.

    2017-12-01

    The Röntgen term is an often neglected contribution to the interaction between an atom and an electromagnetic field in the electric dipole approximation. In this work we discuss how this interaction term leads to a difference between the kinetic and canonical momentum of an atom which, in turn, leads to surprising radiation forces acting on the atom. We use a number of examples to explore the main features of this interaction, namely forces acting against the expected dipole force or accelerations perpendicular to the beam propagation axis.

  2. Theoretical study of the effect of probe shape on adhesion force between probe and substrate in atomic force microscope experiment

    OpenAIRE

    Yang, Li; Hu, Junhui; Kong, Lingjiang

    2017-01-01

    The quantitative description of adhesion force dependence on the probe shapes are of importance in many scientific and industrial fields. In order to elucidate how the adhesion force varied with the probe shape in atomic force microscope manipulation experiment, we performed a theoretical study of the influences of the probe shape (the sphere and parabolic probe) on the adhesion force at different humidity. We found that the combined action of the triple point and the Kelvin radius guiding th...

  3. Rydberg atoms in strong fields

    International Nuclear Information System (INIS)

    Kleppner, D.; Tsimmerman, M.

    1985-01-01

    Experimental and theoretical achievements in studying Rydberg atoms in external fields are considered. Only static (or quasistatic) fields and ''one-electron'' atoms, i.e. atoms that are well described by one-electron states, are discussed. Mainly behaviour of alkali metal atoms in electric field is considered. The state of theoretical investigations for hydrogen atom in magnetic field is described, but experimental data for atoms of alkali metals are presented as an illustration. Results of the latest experimental and theoretical investigations into the structure of Rydberg atoms in strong fields are presented

  4. Automated force controller for amplitude modulation atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Miyagi, Atsushi, E-mail: atsushi.miyagi@inserm.fr, E-mail: simon.scheuring@inserm.fr; Scheuring, Simon, E-mail: atsushi.miyagi@inserm.fr, E-mail: simon.scheuring@inserm.fr [U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13009 Marseille (France)

    2016-05-15

    Atomic Force Microscopy (AFM) is widely used in physics, chemistry, and biology to analyze the topography of a sample at nanometer resolution. Controlling precisely the force applied by the AFM tip to the sample is a prerequisite for faithful and reproducible imaging. In amplitude modulation (oscillating) mode AFM, the applied force depends on the free and the setpoint amplitudes of the cantilever oscillation. Therefore, for keeping the applied force constant, not only the setpoint amplitude but also the free amplitude must be kept constant. While the AFM user defines the setpoint amplitude, the free amplitude is typically subject to uncontrollable drift, and hence, unfortunately, the real applied force is permanently drifting during an experiment. This is particularly harmful in biological sciences where increased force destroys the soft biological matter. Here, we have developed a strategy and an electronic circuit that analyzes permanently the free amplitude of oscillation and readjusts the excitation to maintain the free amplitude constant. As a consequence, the real applied force is permanently and automatically controlled with picoNewton precision. With this circuit associated to a high-speed AFM, we illustrate the power of the development through imaging over long-duration and at various forces. The development is applicable for all AFMs and will widen the applicability of AFM to a larger range of samples and to a larger range of (non-specialist) users. Furthermore, from controlled force imaging experiments, the interaction strength between biomolecules can be analyzed.

  5. Cooperatively enhanced dipole forces from artificial atoms in trapped nanodiamonds

    Science.gov (United States)

    Juan, Mathieu L.; Bradac, Carlo; Besga, Benjamin; Johnsson, Mattias; Brennen, Gavin; Molina-Terriza, Gabriel; Volz, Thomas

    2017-03-01

    Optical trapping is a powerful tool to manipulate small particles, from micrometre-size beads in liquid environments to single atoms in vacuum. The trapping mechanism relies on the interaction between a dipole and the electric field of laser light. In atom trapping, the dominant contribution to the associated force typically comes from the allowed optical transition closest to the laser wavelength, whereas for mesoscopic particles it is given by the polarizability of the bulk material. Here, we show that for nanoscale diamond crystals containing a large number of artificial atoms, nitrogen-vacancy colour centres, the contributions from both the nanodiamond and the colour centres to the optical trapping strength can be simultaneously observed in a noisy liquid environment. For wavelengths around the zero-phonon line transition of the colour centres, we observe a 10% increase of overall trapping strength. The magnitude of this effect suggests that due to the large density of centres, cooperative effects between the artificial atoms contribute to the observed modification of the trapping strength. Our approach may enable the study of cooperativity in nanoscale solid-state systems and the use of atomic physics techniques in the field of nano-manipulation.

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

    Science.gov (United States)

    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.

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

    International Nuclear Information System (INIS)

    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

  8. Manipulating beams of ultra-cold atoms with a static magnetic field

    International Nuclear Information System (INIS)

    Rowlands, W.J.; Lau, D.C.; Opat, G.I.; Sidorov, A.I.; McLean, R.J.; Hannaford, P.

    1996-01-01

    The preliminary results on the deflection of a beam of ultra-cold atoms by a static magnetic field are presented. Caesium atoms trapped in a magneto-optical trap (MOT) are cooled using optical molasses, and then fall freely under gravity to form a beam of ultra-cold atoms. The atoms pass through a static inhomogeneous magnetic field produced by a single current-carrying wire, and are deflected by a force dependent on the magnetic substate of the atom. A schematical diagram of the experimental layout for laser trapping and cooling of cesium atom is given. The population of atoms in various magnetic substates can be altered by using resonant laser radiation to optically pump the atoms. The single-wire deflection experiment described can be considered as atomic reflexion from a cylindrical magnetic mirror; the underlying principles and techniques being relevant to the production of atomic mirrors and diffraction gratings. 16 refs., 10 figs

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

    Science.gov (United States)

    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.

  10. Atom dynamics in laser fields

    International Nuclear Information System (INIS)

    Jang, Su; Mi, No Gin

    2004-12-01

    This book introduces coherent dynamics of internal state, spread of atoms wave speed, semiclassical atoms density matrix such as dynamics equation in both still and moving atoms, excitation of atoms in movement by light, dipole radiating power, quantum statistical mechanics by atoms in movement, semiclassical atoms in movement, atoms in movement in the uniform magnetic field including effects of uniform magnetic field, atom cooling using laser such as Doppler cooling, atom traps using laser and mirrors, radiant heat which particles receive, and near field interactions among atoms in laser light.

  11. 5. All-Russian (international) scientific conference. Physicochemical processes during selection of atoms and molecules. Collection of reports

    International Nuclear Information System (INIS)

    Baranov, V.Yu.; Kolesnikov, Yu.A.

    2000-01-01

    The materials of the 5. All-Russian (international) scientific conference: Physicochemical processes during selection of atoms and molecules, are presented. The conference took place in Zvenigorod, 2-6 October, 2000. A wide range of items connected with uranium enrichment, selection of atoms and molecules by isotopic composition: laser methods, ion cyclotron-resonance method, are discussed. The selection of molecules and atoms by rectification and chemical isotopic exchange methods, the selection in the field of centrifugal forces are treated. The questions of search for the new advanced methods for selection of atoms and molecules were discussed at the conference, the problems of radioisotope production were represented. The subject matter of the use of stable isotopes and radionuclides is demonstrated widely. The subjects connected with experimental and engineering equipment for selection of atoms and molecules are embodied in the paper [ru

  12. All-atom simulation study of protein PTH(1-34) by using the Wang-Landau sampling method

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Seung-Yeon [Korea National University of Transportation, Chungju (Korea, Republic of); Kwak, Woo-Seop [Chosun University, Gwangju (Korea, Republic of)

    2014-12-15

    We perform simulations of the N-terminal 34-residue protein fragment PTH(1-34), consisting of 581 atoms, of the 84-residue human parathyroid hormone by using the all-atom ECEPP/3 force field and the Wang-Landau sampling method. Through a massive high-performance computation, the density of states and the partition function Z(T), as a continuous function of T, are obtained for PTH(1-34). From the continuous partition function Z(T), the partition function zeros of PTH(1-34) are evaluated for the first time. From both the specific heat and the partition function zeros, two characteristic transition temperatures are obtained for the all-atom protein PTH(1-34). The higher transition temperature T{sub 1} and the lower transition temperature T{sub 2} of PTH(1-34) can be interpreted as the collapse temperature T{sub θ} and the folding temperature T{sub f} , respectively.

  13. The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

    International Nuclear Information System (INIS)

    Cortini, Ruggero; Cheng, Xiaolin

    2017-01-01

    Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning's theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order of 1k B T. Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.

  14. Refined tip preparation by electrochemical etching and ultrahigh vacuum treatment to obtain atomically sharp tips for scanning tunneling microscope and atomic force microscope

    International Nuclear Information System (INIS)

    Hagedorn, Till; Ouali, Mehdi El; Paul, William; Oliver, David; Miyahara, Yoichi; Gruetter, Peter

    2011-01-01

    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.

  15. Measuring Forces between Oxide Surfaces Using the Atomic Force Microscope

    DEFF Research Database (Denmark)

    Pedersen, Henrik Guldberg; Høj, Jakob Weiland

    1996-01-01

    The interactions between colloidal particles play a major role in processing of ceramics, especially in casting processes. With the Atomic Force Microscope (AFM) it is possible to measure the inter-action force between a small oxide particle (a few micron) and a surface as function of surface...

  16. Van der Waals Forces and Photon-Less Effective Field Theory

    International Nuclear Information System (INIS)

    Arriola, E.R.

    2011-01-01

    In the ultra-cold regime Van der Waals forces between neutral atoms can be represented by short range effective interactions. We show that universal low energy scaling features of the underlying vdW long range force stemming from two photon exchange impose restrictions on an Effective Field Theory without explicit photons. The role of naively redundant operators, relevant to the definition of three body forces, is also analyzed. (author)

  17. Calcite biomineralization in coccoliths: Evidence from atomic force microscopy (AFM)

    DEFF Research Database (Denmark)

    Henriksen, Karen; Stipp, S.L.S.

    2002-01-01

    geochemistry, crystal orientation, coccolith function, biomineralization, biological calcite, atomic force microscopy......geochemistry, crystal orientation, coccolith function, biomineralization, biological calcite, atomic force microscopy...

  18. Sub-Angstrom oscillation amplitude non-contact atomic force microscopy for lateral force gradient measurement

    International Nuclear Information System (INIS)

    Atabak, Mehrdad; Unverdi, Ozhan; Ozer, H. Ozguer; Oral, Ahmet

    2009-01-01

    We report the first results from novel sub-Angstrom oscillation amplitude non-contact atomic force microscopy developed for lateral force gradient measurements. Quantitative lateral force gradients between a tungsten tip and Si(1 1 1)-(7 x 7) surface can be measured using this microscope. Simultaneous lateral force gradient and scanning tunnelling microscope images of single and multi atomic steps are obtained. In our measurement, tunnel current is used as feedback. The lateral stiffness contrast has been observed to be 2.5 N/m at single atomic step, in contrast to 13 N/m at multi atomic step on Si(1 1 1) surface. We also carried out a series of lateral stiffness-distance spectroscopy. We observed lateral stiffness-distance curves exhibit sharp increase in the stiffness as the sample is approached towards the surface. We usually observed positive stiffness and sometimes going into slightly negative region.

  19. Corrected direct force balance method for atomic force microscopy lateral force calibration

    International Nuclear Information System (INIS)

    Asay, David B.; Hsiao, Erik; Kim, Seong H.

    2009-01-01

    This paper reports corrections and improvements of the previously reported direct force balance method (DFBM) developed for lateral calibration of atomic force microscopy. The DFBM method employs the lateral force signal obtained during a force-distance measurement on a sloped surface and relates this signal to the applied load and the slope of the surface to determine the lateral calibration factor. In the original publication [Rev. Sci. Instrum. 77, 043903 (2006)], the tip-substrate contact was assumed to be pinned at the point of contact, i.e., no slip along the slope. In control experiments, the tip was found to slide along the slope during force-distance curve measurement. This paper presents the correct force balance for lateral force calibration.

  20. Resonant difference-frequency atomic force ultrasonic microscope

    Science.gov (United States)

    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.

  1. Optical Near-field Interactions and Forces for Optoelectronic Devices

    Science.gov (United States)

    Kohoutek, John Michael

    Throughout history, as a particle view of the universe began to take shape, scientists began to realize that these particles were attracted to each other and hence came up with theories, both analytical and empirical in nature, to explain their interaction. The interaction pair potential (empirical) and electromagnetics (analytical) theories, both help to explain not only the interaction between the basic constituents of matter, such as atoms and molecules, but also between macroscopic objects, such as two surfaces in close proximity. The electrostatic force, optical force, and Casimir force can be categorized as such forces. A surface plasmon (SP) is a collective motion of electrons generated by light at the interface between two mediums of opposite signs of dielectric susceptibility (e.g. metal and dielectric). Recently, surface plasmon resonance (SPR) has been exploited in many areas through the use of tiny antennas that work on similar principles as radio frequency (RF) antennas in optoelectronic devices. These antennas can produce a very high gradient in the electric field thereby leading to an optical force, similar in concept to the surface forces discussed above. The Atomic Force Microscope (AFM) was introduced in the 1980s at IBM. Here we report on its uses in measuring these aforementioned forces and fields, as well as actively modulating and manipulating multiple optoelectronic devices. We have shown that it is possible to change the far field radiation pattern of an optical antenna-integrated device through modification of the near-field of the device. This modification is possible through change of the local refractive index or reflectivity of the "hot spot" of the device, either mechanically or optically. Finally, we have shown how a mechanically active device can be used to detect light with high gain and low noise at room temperature. It is the aim of several of these integrated and future devices to be used for applications in molecular sensing

  2. On the role of coulomb forces in atomic radiative emission

    International Nuclear Information System (INIS)

    Yngstroem, S.

    1988-10-01

    It is shown how the generalized Coulomb interaction (electric and magnetic fields of force) competes with the radiative interaction causing overall inhibition of the radiative capability of atoms and ions in a gaseous sample of matter. Basic quantum mechanical aspects of the electromagnetic interaction are discussed in a heuristic introduction followed by a more precise treatment in the formalism of relativistic quantum electrodynamics. (author)

  3. Atomic Force Microscopy Application in Biological Research: A Review Study

    Directory of Open Access Journals (Sweden)

    Surena Vahabi

    2013-06-01

    Full Text Available Atomic force microscopy (AFM is a three-dimensional topographic technique with a high atomic resolution to measure surface roughness. AFM is a kind of scanning probe microscope, and its near-field technique is based on the interaction between a sharp tip and the atoms of the sample surface. There are several methods and many ways to modify the tip of the AFM to investigate surface properties, including measuring friction, adhesion forces and viscoelastic properties as well as determining the Young modulus and imaging magnetic or electrostatic properties. The AFM technique can analyze any kind of samples such as polymers, adsorbed molecules, films or fibers, and powders in the air whether in a controlled atmosphere or in a liquid medium. In the past decade, the AFM has emerged as a powerful tool to obtain the nanostructural details and biomechanical properties of biological samples, including biomolecules and cells. The AFM applications, techniques, and -in particular- its ability to measure forces, are not still familiar to most clinicians. This paper reviews the literature on the main principles of the AFM modality and highlights the advantages of this technique in biology, medicine, and- especially- dentistry. This literature review was performed through E-resources, including Science Direct, PubMed, Blackwell Synergy, Embase, Elsevier, and Scholar Google for the references published between 1985 and 2010.

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

    Science.gov (United States)

    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

  5. Fidelity imaging for atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ghosal, Sayan, E-mail: ghos0087@umn.edu; Salapaka, Murti, E-mail: murtis@umn.edu [Nanodynamics Systems Laboratory, Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (United States)

    2015-01-05

    Atomic force microscopy is widely employed for imaging material at the nanoscale. However, real-time measures on image reliability are lacking in contemporary atomic force microscopy literature. In this article, we present a real-time technique that provides an image of fidelity for a high bandwidth dynamic mode imaging scheme. The fidelity images define channels that allow the user to have additional authority over the choice of decision threshold that facilitates where the emphasis is desired, on discovering most true features on the sample with the possible detection of high number of false features, or emphasizing minimizing instances of false detections. Simulation and experimental results demonstrate the effectiveness of fidelity imaging.

  6. Principles and applications of force spectroscopy using atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Young Kyu; Kim, Woong; Park, Joon Won [Dept. of Chemistry, Pohang University of Science and Technology, Pohang (Korea, Republic of)

    2016-12-15

    Single-molecule force spectroscopy is a powerful technique for addressing single molecules. Unseen structures and dynamics of molecules have been elucidated using force spectroscopy. Atomic force microscope (AFM)-based force spectroscopy studies have provided picoNewton force resolution, subnanometer spatial resolution, stiffness of substrates, elasticity of polymers, and thermodynamics and kinetics of single-molecular interactions. In addition, AFM has enabled mapping the distribution of individual molecules in situ, and the quantification of single molecules has been made possible without modification or labeling. In this review, we describe the basic principles, sample preparation, data analysis, and applications of AFM-based force spectroscopy and its future.

  7. Refined tip preparation by electrochemical etching and ultrahigh vacuum treatment to obtain atomically sharp tips for scanning tunneling microscope and atomic force microscope.

    Science.gov (United States)

    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

  8. Capillary forces in tapping mode atomic force microscopy

    NARCIS (Netherlands)

    Zitzler, L.; Herminghaus, S.; Mugele, Friedrich Gunther

    2002-01-01

    We investigated the influence of the relative humidity on amplitude and phase of the cantilever oscillation while operating an atomic force microscope (AFM) in the tapping mode. If the free oscillation amplitude A0 exceeds a certain critical amplitude Ac, the amplitude- and phase-distance curves

  9. High-magnetic field atomic physics

    International Nuclear Information System (INIS)

    Gay, J.C.

    1984-01-01

    This chapter discusses both the traditional developments of Zeeman techniques at strong fields and the fundamental concepts of diamagnetism. Topics considered include historical aspects, the production of high fields, the atom in a magnetic field (Hamiltonian and symmetries, the various magnetic regimes in atomic spectra), applications of the Zeeman effect at strong B fields, the Landau regime for loosely bound particles, theoretical concepts of atomic diamagnetism, and the ultra-high-field regime and quantum electrodynamics. It is concluded that the wide implications of the problem of the strongly magnetized hydrogen atom in various domains of physics and its conceptual importance concerning theoretical methods of classical and quantum mechanics justify the experimental and theoretical efforts in atomic physics

  10. Dissipation and oscillatory solvation forces in confined liquids studied by small amplitude atomic force spectroscopy

    NARCIS (Netherlands)

    de Beer, Sissi; van den Ende, Henricus T.M.; Mugele, Friedrich

    2010-01-01

    We determine conservative and dissipative tip–sample interaction forces from the amplitude and phase response of acoustically driven atomic force microscope (AFM) cantilevers using a non-polar model fluid (octamethylcyclotetrasiloxane, which displays strong molecular layering) and atomically flat

  11. Immunogold labels: cell-surface markers in atomic force microscopy

    NARCIS (Netherlands)

    Putman, Constant A.J.; Putman, C.A.J.; de Grooth, B.G.; Hansma, Paul K.; van Hulst, N.F.; Greve, Jan

    1993-01-01

    The feasibility of using immunogold labels as cell-surface markers in atomic force microscopy is shown in this paper. The atomic force microscope (AFM) was used to image the surface of immunogold-labeled human lymphocytes. The lymphocytes were isolated from whole blood and labeled by an indirect

  12. Structure and stability of semiconductor tip apexes for atomic force microscopy

    International Nuclear Information System (INIS)

    Pou, P; Perez, R; Ghasemi, S A; Goedecker, S; Jelinek, P; Lenosky, T

    2009-01-01

    The short range force between the tip and the surface atoms, that is responsible for atomic-scale contrast in atomic force microscopy (AFM), is mainly controlled by the tip apex. Thus, the ability to image, manipulate and chemically identify single atoms in semiconductor surfaces is ultimately determined by the apex structure and its composition. Here we present a detailed and systematic study of the most common structures that can be expected at the apex of the Si tips used in experiments. We tackle the determination of the structure and stability of Si tips with three different approaches: (i) first principles simulations of small tip apexes; (ii) simulated annealing of a Si cluster; and (iii) a minima hopping study of large Si tips. We have probed the tip apexes by making atomic contacts between the tips and then compared force-distance curves with the experimental short range forces obtained with dynamic force spectroscopy. The main conclusion is that although there are multiple stable solutions for the atomically sharp tip apexes, they can be grouped into a few types with characteristic atomic structures and properties. We also show that the structure of the last atomic layers in a tip apex can be both crystalline and amorphous. We corroborate that the atomically sharp tips are thermodynamically stable and that the tip-surface interaction helps to produce the atomic protrusion needed to get atomic resolution.

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

    Science.gov (United States)

    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.

  14. High-speed force mapping on living cells with a small cantilever atomic force microscope

    International Nuclear Information System (INIS)

    Braunsmann, Christoph; Seifert, Jan; Rheinlaender, Johannes; Schäffer, Tilman E.

    2014-01-01

    The imaging speed of the wide-spread force mapping mode for quantitative mechanical measurements on soft samples in liquid with the atomic force microscope (AFM) is limited by the bandwidth of the z-scanner and viscous drag forces on the cantilever. Here, we applied high-speed, large scan-range atomic force microscopy and small cantilevers to increase the speed of force mapping by ≈10−100 times. This allowed resolving dynamic processes on living mouse embryonic fibroblasts. Cytoskeleton reorganization during cell locomotion, growth of individual cytoskeleton fibers, cell blebbing, and the formation of endocytic pits in the cell membrane were observed. Increasing the force curve rate from 2 to 300 Hz increased the measured apparent Young's modulus of the cells by about 10 times, which facilitated force mapping measurements at high speed

  15. High-speed force mapping on living cells with a small cantilever atomic force microscope

    Energy Technology Data Exchange (ETDEWEB)

    Braunsmann, Christoph; Seifert, Jan; Rheinlaender, Johannes; Schäffer, Tilman E., E-mail: Tilman.Schaeffer@uni-tuebingen [Institute of Applied Physics and LISA, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen (Germany)

    2014-07-15

    The imaging speed of the wide-spread force mapping mode for quantitative mechanical measurements on soft samples in liquid with the atomic force microscope (AFM) is limited by the bandwidth of the z-scanner and viscous drag forces on the cantilever. Here, we applied high-speed, large scan-range atomic force microscopy and small cantilevers to increase the speed of force mapping by ≈10−100 times. This allowed resolving dynamic processes on living mouse embryonic fibroblasts. Cytoskeleton reorganization during cell locomotion, growth of individual cytoskeleton fibers, cell blebbing, and the formation of endocytic pits in the cell membrane were observed. Increasing the force curve rate from 2 to 300 Hz increased the measured apparent Young's modulus of the cells by about 10 times, which facilitated force mapping measurements at high speed.

  16. Significant improvements in stability and reproducibility of atomic-scale atomic force microscopy in liquid

    International Nuclear Information System (INIS)

    Akrami, S M R; Nakayachi, H; Fukuma, T; Watanabe-Nakayama, T; Asakawa, H

    2014-01-01

    Recent advancement of dynamic-mode atomic force microscopy (AFM) for liquid-environment applications enabled atomic-scale studies on various interfacial phenomena. However, instabilities and poor reproducibility of the measurements often prevent systematic studies. To solve this problem, we have investigated the effect of various tip treatment methods for atomic-scale imaging and force measurements in liquid. The tested methods include Si coating, Ar plasma, Ar sputtering and UV/O 3 cleaning. We found that all the methods provide significant improvements in both the imaging and force measurements in spite of the tip transfer through the air. Among the methods, we found that the Si coating provides the best stability and reproducibility in the measurements. To understand the origin of the fouling resistance of the cleaned tip surface and the difference between the cleaning methods, we have investigated the tip surface properties by x-ray photoelectron spectroscopy and contact angle measurements. The results show that the contaminations adsorbed on the tip during the tip transfer through the air should desorb from the surface when it is immersed in aqueous solution due to the enhanced hydrophilicity by the tip treatments. The tip surface prepared by the Si coating is oxidized when it is immersed in aqueous solution. This creates local spots where stable hydration structures are formed. For the other methods, there is no active mechanism to create such local hydration sites. Thus, the hydration structure formed under the tip apex is not necessarily stable. These results reveal the desirable tip properties for atomic-scale AFM measurements in liquid, which should serve as a guideline for further improvements of the tip treatment methods. (paper)

  17. Accelerating all-atom MD simulations of lipids using a modified virtual-sites technique

    DEFF Research Database (Denmark)

    Loubet, Bastien; Kopec, Wojciech; Khandelia, Himanshu

    2014-01-01

    We present two new implementations of the virtual sites technique which completely suppresses the degrees of freedom of the hydrogen atoms in a lipid bilayer allowing for an increased time step of 5 fs in all-atom simulations of the CHARMM36 force field. One of our approaches uses the derivation...... of the virtual sites used in GROMACS while the other uses a new definition of the virtual sites of the CH2 groups. Our methods is tested on a DPPC (no unsaturated chain), a POPC (one unsaturated chain), and a DOPC (two unsaturated chains) lipid bilayers. We calculate various physical properties of the membrane...... of our simulations with and without virtual sites and explain the differences and similarity observed. The best agreements are obtained for the GROMACS original virtual sites on the DOPC bilayer where we get an area per lipid of 67.3 ± 0.3 A˚2 without virtual sites and 67.6 ± 0.3 A˚2 with virtual sites...

  18. Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme

    International Nuclear Information System (INIS)

    Soares, T. A.; Daura, X.; Oostenbrink, C.; Smith, L. J.; Gunsteren, W. F. van

    2004-01-01

    The quality of molecular dynamics (MD) simulations of proteins depends critically on the biomolecular force field that is used. Such force fields are defined by force-field parameter sets, which are generally determined and improved through calibration of properties of small molecules against experimental or theoretical data. By application to large molecules such as proteins, a new force-field parameter set can be validated. We report two 3.5 ns molecular dynamics simulations of hen egg white lysozyme in water applying the widely used GROMOS force-field parameter set 43A1 and a new set 45A3. The two MD ensembles are evaluated against NMR spectroscopic data NOE atom-atom distance bounds, 3 J NHα and 3 J αβ coupling constants, and 1 5N relaxation data. It is shown that the two sets reproduce structural properties about equally well. The 45A3 ensemble fulfills the atom-atom distance bounds derived from NMR spectroscopy slightly less well than the 43A1 ensemble, with most of the NOE distance violations in both ensembles involving residues located in loops or flexible regions of the protein. Convergence patterns are very similar in both simulations atom-positional root-mean-square differences (RMSD) with respect to the X-ray and NMR model structures and NOE inter-proton distances converge within 1.0-1.5 ns while backbone 3 J HNα -coupling constants and 1 H- 1 5N order parameters take slightly longer, 1.0-2.0 ns. As expected, side-chain 3 J αβ -coupling constants and 1 H- 1 5N order parameters do not reach full convergence for all residues in the time period simulated. This is particularly noticeable for side chains which display rare structural transitions. When comparing each simulation trajectory with an older and a newer set of experimental NOE data on lysozyme, it is found that the newer, larger, set of experimental data agrees as well with each of the simulations. In other words, the experimental data converged towards the theoretical result

  19. Machine learning of accurate energy-conserving molecular force fields

    Science.gov (United States)

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

    2017-01-01

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

  20. Electric field imaging of single atoms

    Science.gov (United States)

    Shibata, Naoya; Seki, Takehito; Sánchez-Santolino, Gabriel; Findlay, Scott D.; Kohno, Yuji; Matsumoto, Takao; Ishikawa, Ryo; Ikuhara, Yuichi

    2017-01-01

    In scanning transmission electron microscopy (STEM), single atoms can be imaged by detecting electrons scattered through high angles using post-specimen, annular-type detectors. Recently, it has been shown that the atomic-scale electric field of both the positive atomic nuclei and the surrounding negative electrons within crystalline materials can be probed by atomic-resolution differential phase contrast STEM. Here we demonstrate the real-space imaging of the (projected) atomic electric field distribution inside single Au atoms, using sub-Å spatial resolution STEM combined with a high-speed segmented detector. We directly visualize that the electric field distribution (blurred by the sub-Å size electron probe) drastically changes within the single Au atom in a shape that relates to the spatial variation of total charge density within the atom. Atomic-resolution electric field mapping with single-atom sensitivity enables us to examine their detailed internal and boundary structures. PMID:28555629

  1. Raman-atomic force microscopy of the ommatidial surfaces of Dipteran compound eyes

    Science.gov (United States)

    Anderson, Mark S.; Gaimari, Stephen D.

    2003-01-01

    The ommatidial lens surfaces of the compound eyes in several species of files (Insecta: Diptera) and a related order (Mecoptera) were analyzed using a recently developed Raman-atomic force microscope. We demonstrate in this work that the atomic force microscope (AFM) is a potentially useful instrument for gathering phylogenetic data and that the newly developed Raman-AFM may extend this application by revealing nanometer-scale surface chemistry. This is the first demonstration of apertureless near-field Raman spectroscopy on an intact biological surface. For Chrysopilus testaceipes Bigot (Rhagionidae), this reveals unique cerebral cortex-like surface ridges with periodic variation in height and surface chemistry. Most other Brachyceran flies, and the "Nematoceran" Sylvicola fenestralis (Scopoli) (Anisopodidae), displayed the same morphology, while other taxa displayed various other characteristics, such as a nodule-like (Tipula (Triplicitipula) sp. (Tipulidae)) or coalescing nodule-like (Tabanus punctifer Osten Sacken (Tabanidae)) morphology, a smooth morphology with distinct pits and grooves (Dilophus orbatus (Say) (Bibionidae)), or an entirely smooth surface (Bittacus chlorostigma MacLachlan (Mecoptera: Bittacidae)). The variation in submicrometer structure and surface chemistry provides a new information source of potential phylogenetic importance, suggesting the Raman-atomic force microscope could provide a new tool useful to systematic and evolutionary inquiry.

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

    Science.gov (United States)

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

    2015-01-01

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

  3. Capillary force on a tilted cylinder: Atomic Force Microscope (AFM) measurements.

    Science.gov (United States)

    Kosgodagan Acharige, Sébastien; Laurent, Justine; Steinberger, Audrey

    2017-11-01

    The capillary force in situations where the liquid meniscus is asymmetric, such as the one around a tilted object, has been hitherto barely investigated even though these situations are very common in practice. In particular, the capillary force exerted on a tilted object may depend on the dipping angle i. We investigate experimentally the capillary force that applies on a tilted cylinder as a function of its dipping angle i, using a home-built tilting Atomic Force Microscope (AFM) with custom made probes. A micrometric-size rod is glued at the end of an AFM cantilever of known stiffness, whose deflection is measured when the cylindrical probe is dipped in and retracted from reference liquids. We show that a torque correction is necessary to understand the measured deflection. We give the explicit expression of this correction as a function of the probes' geometrical parameters, so that its magnitude can be readily evaluated. The results are compatible with a vertical capillary force varying as 1/cosi, in agreement with a recent theoretical prediction. Finally, we discuss the accuracy of the method for measuring the surface tension times the cosine of the contact angle of the liquid on the probe. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Low-energy oxygen bombardment of silicon by MD simulations making use of a reactive force field

    International Nuclear Information System (INIS)

    Philipp, P.; Briquet, L.; Wirtz, T.; Kieffer, J.

    2011-01-01

    In the field of Secondary Ion Mass Spectrometry (SIMS), ion-matter interactions have been largely investigated by numerical simulations. For MD simulations related to inorganic samples, mostly classical force fields assuming stable bonding structure have been used. In materials science, level-three force fields capable of simulating the breaking and formation of chemical bonds have recently been conceived. One such force field has been developed by John Kieffer . This potential includes directional covalent bonds, Coulomb and dipolar interaction terms, dispersion terms, etc. Important features of this force field for simulating systems that undergo significant structural reorganization are (i) the ability to account for the redistribution of electron density upon ionization, formation, or breaking of bonds, through a charge transfer term, and (ii) the fact that the angular constraints dynamically adjust when a change in the coordination number of an atom occurs. In this paper, the modification of the force field to allow for an exact description of the sputtering process, the influence of this modification on previous results obtained for phase transitions in glasses as well as properties of particles sputtered at 250-1000 eV from a mono-crystalline silicon sample will be presented. The simulation results agree qualitatively with predictions from experiments or models. Most atoms are sputtered from the first monolayer: for an impact energy of 250 eV up to 86% of the atoms are sputtered from the first monolayer and for 750 eV, this percentage drops to 61%, with 89% of the atoms being sputtered from the first two monolayers. For sputtering yields, 250 and 500 eV results agree with experimental data, but for 750 eV sub-channelling in the pristine sample becomes more important than in experiments where samples turn amorphous under ion bombardment.

  5. Correlated motion of two atoms trapped in a single-mode cavity field

    International Nuclear Information System (INIS)

    Asboth, Janos K.; Domokos, Peter; Ritsch, Helmut

    2004-01-01

    We study the motion of two atoms trapped at distant positions in the field of a driven standing-wave high-Q optical resonator. Even without any direct atom-atom interaction the atoms are coupled through their position dependent influence on the intracavity field. For sufficiently good trapping and low cavity losses the atomic motion becomes significantly correlated and the two particles oscillate in their wells preferentially with a 90 deg. relative phase shift. The onset of correlations seriously limits cavity cooling efficiency, raising the achievable temperature to the Doppler limit. The physical origin of the correlation can be traced back to a cavity mediated crossfriction, i.e., a friction force on one particle depending on the velocity of the second particle. Choosing appropriate operating conditions allows for engineering these long range correlations. In addition this cross-friction effect can provide a basis for sympathetic cooling of distant trapped clouds

  6. Adhesion force imaging in air and liquid by adhesion mode atomic force microscopy

    NARCIS (Netherlands)

    van der Werf, Kees; Putman, C.A.J.; Putman, Constant A.; de Grooth, B.G.; Greve, Jan

    1994-01-01

    A new imaging mode for the atomic force microscope(AFM), yielding images mapping the adhesion force between tip and sample, is introduced. The adhesion mode AFM takes a force curve at each pixel by ramping a piezoactuator, moving the silicon‐nitride tip up and down towards the sample. During the

  7. Functionalization of gold and nanocrystalline diamond atomic force microscope tips for single molecule force spectroscopy

    Science.gov (United States)

    Drew, Michael E.

    The atomic force microscope (AFM) has fueled interest in nanotechnology because of its ability to image surfaces at the nanometer level and act as a molecular force sensor. Functionalization of the surface of an AFM tip surface in a stable, controlled manner expands the capabilities of the AFM and enables additional applications in the fields of single molecule force spectroscopy and nanolithography. Two AFM tip functionalizations are described: the assembly of tripodal molecular tips onto gold AFM tips and the photochemical attachment of terminal alkenes to nanocrystalline diamond (NCD) AFM tips. Two separate tripodal molecules with different linker lengths and a monopodal molecule terminated with biotin were synthesized to attach to a gold AFM tip for single molecule force spectroscopy. The immobilization of these molecules was examined by contact angle measurements, spectroscopic ellipsometry, infrared, and near edge x-ray absorption fine structure (NEXAFS) spectroscopy. All three molecules displayed rupture forces that agreed with previously reported values for the biotin--avidin rupture. The tripodal molecular tip displayed narrower distribution in their force histograms than the monopodal molecular tip. The performance of the tripodal molecular tip was compared to the monopodal molecular tip in single molecule force spectroscopy studies. Over repeated measurements, the distribution of forces for the monopodal molecular tip shifted to lower forces, whereas the distribution for the tripodal molecular tip remained constant throughout. Loading rate dependence and control experiments further indicated that the rupture forces of the tripod molecular tips were specific to the biotin--NeutrAvidin interaction. The second functionalization method used the photochemical attachment of undecylenic acid to NCD AFM tips. The photochemical attachment of undecylenic acid to hydrogen-terminated NCD wafer surfaces was investigated by contact angle measurements, x

  8. The contribution of the electrostatic proximity force to atomic force microscopy with insulators

    International Nuclear Information System (INIS)

    Stanley Czarnecki, W.; Schein, L.B.

    2005-01-01

    Measurements, using atomic force microscopy, of the force and force derivative on a charged insulating micron sized sphere as a function of gap between the sphere and a conductive plane have revealed attractive forces at finite gaps that are larger than predicted by either van der Waals or conventional electrostatic forces. We suggest that these observations may be due to an electrostatic force that we have identified theoretically and call the proximity force. This proximity force is due to the discrete charges on the surface of the sphere in close proximity to the plane

  9. The contribution of the electrostatic proximity force to atomic force microscopy with insulators

    Energy Technology Data Exchange (ETDEWEB)

    Stanley Czarnecki, W. [Aetas Technology Corporation, P.O. Box 53398, Irvine, CA 92619-3398 (United States); IBM Corporation, 5600 Cottle Rd., Building 13, San Jose, CA 95193 (United States); Schein, L.B. [Aetas Technology Corporation, P.O. Box 53398, Irvine, CA 92619-3398 (United States)]. E-mail: schein@prodigy.net

    2005-05-16

    Measurements, using atomic force microscopy, of the force and force derivative on a charged insulating micron sized sphere as a function of gap between the sphere and a conductive plane have revealed attractive forces at finite gaps that are larger than predicted by either van der Waals or conventional electrostatic forces. We suggest that these observations may be due to an electrostatic force that we have identified theoretically and call the proximity force. This proximity force is due to the discrete charges on the surface of the sphere in close proximity to the plane.

  10. Atomic imaging of an InSe single-crystal surface with atomic force microscope

    OpenAIRE

    Uosaki, Kohei; Koinuma, Michio

    1993-01-01

    The atomic force microscope was employed to observed in air the surface atomic structure of InSe, one of III-VI compound semiconductors with layered structures. Atomic arrangements were observed in both n-type and p-type materials. The observed structures are in good agreement with those expected from bulk crystal structures. The atomic images became less clear by repeating the imaging process. Wide area imaging after the imaging of small area clearly showed that a mound was created at the sp...

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

    Directory of Open Access Journals (Sweden)

    Adam Sweetman

    2014-04-01

    Full Text Available 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.

  12. Molecular Processes Studied at a Single-Molecule Level Using DNA Origami Nanostructures and Atomic Force Microscopy

    Directory of Open Access Journals (Sweden)

    Ilko Bald

    2014-09-01

    Full Text Available DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.

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

    Energy Technology Data Exchange (ETDEWEB)

    Usui, Kota; Nagata, Yuki, E-mail: sulpizi@uni-mainz.de, E-mail: nagata@mpip-mainz.mpg.de; Hunger, Johannes; Bonn, Mischa [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany); Sulpizi, Marialore, E-mail: sulpizi@uni-mainz.de, E-mail: nagata@mpip-mainz.mpg.de [Johannes Gutenberg University Mainz, Staudingerweg 7, 55099 Mainz (Germany)

    2016-08-14

    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 increasing 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.

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

    International Nuclear Information System (INIS)

    Usui, Kota; Nagata, Yuki; Hunger, Johannes; Bonn, Mischa; Sulpizi, Marialore

    2016-01-01

    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 TMAO ) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around O TMAO to mimic the O TMAO lone pairs and we migrate the negative charge on the O 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 increasing 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.

  15. Study of Adhesion Interaction Using Atomic Force Microscopy

    Science.gov (United States)

    Grybos, J.; Pyka-Fosciak, G.; Lebed, K.; Lekka, M.; Stachura, Z.; Styczeñ, J.

    2003-05-01

    An atomic force microscope is a useful tool to study the interaction forces at molecular level. In particular the atomic force microscope can measure an unbinding force needed to separate the two single molecule complexes. Recent studies have shown that such unbinding force depends linearly on the logarithm of the applied loading rate, defined as a product of scanning velocity and the spring constant characterizing the investigated system (cantilever vs. surface). This dependence can be used to study the energy landscape shape of a molecular complex by the estimation of energy barrier locations and the related dissociation rates. In the present work the complex consisting of ethylene(di)aminetetraacetic acid and the bovine serum albumin was measured. The dependence between the unbinding force and the logarithm of the loading rate was linear. Using the Bell model describing the dissociation of the above molecules caused by the action of the external bond breaking force, two parameters were estimated: the dissociation rate and the position of the energy barrier needed to overcome during a transition from a bound to unbound state. The obtained results are similar to those obtained for a typical ligand--receptor interaction.

  16. Coffee Cup Atomic Force Microscopy

    Science.gov (United States)

    Ashkenaz, David E.; Hall, W. Paige; Haynes, Christy L.; Hicks, Erin M.; McFarland, Adam D.; Sherry, Leif J.; Stuart, Douglas A.; Wheeler, Korin E.; Yonzon, Chanda R.; Zhao, Jing; Godwin, Hilary A.; Van Duyne, Richard P.

    2010-01-01

    In this activity, students use a model created from a coffee cup or cardstock cutout to explore the working principle of an atomic force microscope (AFM). Students manipulate a model of an AFM, using it to examine various objects to retrieve topographic data and then graph and interpret results. The students observe that movement of the AFM…

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

    Science.gov (United States)

    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…

  18. Cooling and trapping neutral atoms with radiative forces

    International Nuclear Information System (INIS)

    Bagnato, V.S.; Castro, J.C.; Li, M.S.; Zilio, S.C.

    1988-01-01

    Techniques to slow and trap neutral atoms at high densities with radiative forces are discussed in this review articles. Among several methods of laser cooling, it is emphasized Zeeman Tuning of the electronic levels and frequency-sweeping techniques. Trapping of neutral atoms and recent results obtained in light and magnetic traps are discussed. Techniques to further cool atoms inside traps are presented and the future of laser cooling of neutral atoms by means of radiation pressure is discussed. (A.C.A.S.) [pt

  19. Effective field theory for cold atoms

    International Nuclear Information System (INIS)

    Hammer, H.-W.

    2005-01-01

    Effective Field Theory (EFT) provides a powerful framework that exploits a separation of scales in physical systems to perform systematically improvable, model-independent calculations. Particularly interesting are few-body systems with short-range interactions and large two-body scattering length. Such systems display remarkable universal features. In systems with more than two particles, a three-body force with limit cycle behavior is required for consistent renormalization already at leading order. We will review this EFT and some of its applications in the physics of cold atoms. Recent extensions of this approach to the four-body system and N-boson droplets in two spatial dimensions will also be discussed

  20. Interactive forces between lignin and cellulase as determined by atomic force microscopy

    OpenAIRE

    Qin, Chengrong; Clarke, Kimberley; Li, Kecheng

    2014-01-01

    Background Lignin is a complex polymer which inhibits the enzymatic conversion of cellulose to glucose in lignocellulose biomass for biofuel production. Cellulase enzymes irreversibly bind to lignin, deactivating the enzyme and lowering the overall activity of the hydrolyzing reaction solution. Within this study, atomic force microscopy (AFM) is used to compare the adhesion forces between cellulase and lignin with the forces between cellulase and cellulose, and to study the moiety groups invo...

  1. Frequency-dependent local field factors in dielectric liquids by a polarizable force field and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Davari, Nazanin; Haghdani, Shokouh; Åstrand, Per-Olof

    2015-01-01

    A force field model for calculating local field factors, i.e. the linear response of the local electric field for example at a nucleus in a molecule with respect to an applied electric field, is discussed. It is based on a combined charge-transfer and point-dipole interaction model for the polarizability, and thereby it includes two physically distinct terms for describing electronic polarization: changes in atomic charges arising from transfer of charge between the atoms and atomic induced dipole moments. A time dependence is included both for the atomic charges and the atomic dipole moments and if they are assumed to oscillate with the same frequency as the applied electric field, a model for frequency-dependent properties are obtained. Furthermore, if a life-time of excited states are included, a model for the complex frequency-dependent polariability is obtained including also information about excited states and the absorption spectrum. We thus present a model for the frequency-dependent local field factors through the first molecular excitation energy. It is combined with molecular dynamics simulations of liquids where a large set of configurations are sampled and for which local field factors are calculated. We are normally not interested in the average of the local field factor but rather in configurations where it is as high as possible. In electrical insulation, we would like to avoid high local field factors to reduce the risk for electrical breakdown, whereas for example in surface-enhanced Raman spectroscopy, high local field factors are desired to give dramatically increased intensities

  2. Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel

    Science.gov (United States)

    Li, Xianfeng; Murthy, N. Sanjeeva; Becker, Matthew L.; Latour, Robert A.

    2016-01-01

    A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications. PMID:27013229

  3. Atoms in strong laser fields

    International Nuclear Information System (INIS)

    L'Huillier, A.

    2002-01-01

    When a high-power laser focuses into a gas of atoms, the electromagnetic field becomes of the same magnitude as the Coulomb field which binds a 1s electron in a hydrogen atom. 3 highly non-linear phenomena can happen: 1) ATI (above threshold ionization): electrons initially in the ground state absorb a large number of photons, many more than the minimum number required for ionization; 2) multiple ionization: many electrons can be emitted one at a time, in a sequential process, or simultaneously in a mechanism called direct or non-sequential; and 3) high order harmonic generation (HHG): efficient photon emission in the extreme ultraviolet range, in the form of high-order harmonics of the fundamental laser field can occur. The theoretical problem consists in solving the time dependent Schroedinger equation (TDSE) that describes the interaction of a many-electron atom with a laser field. A number of methods have been proposed to solve this problem in the case of a hydrogen atom or a single-active electron atom in a strong laser field. A large effort is presently being devoted to go beyond the single-active approximation. The understanding of the physics of the interaction between atoms and strong laser fields has been provided by a very simple model called ''simple man's theory''. A unified view of HHG, ATI, and non-sequential ionization, originating from the simple man's model and the strong field approximation, expressed in terms of electrons trajectories or quantum paths is slowly emerging. (A.C.)

  4. Atomic force microscopy for university students: applications in biomaterials

    International Nuclear Information System (INIS)

    Kontomaris, S V; Stylianou, A

    2017-01-01

    Atomic force microscopy (AFM) is a powerful tool used in the investigation of the structural and mechanical properties of a wide range of materials including biomaterials. It provides the ability to acquire high resolution images of biomaterials at the nanoscale. It also provides information about the response of specific areas under controlled applied force, which leads to the mechanical characterization of the sample at the nanoscale. The wide range of information provided by AFM has established it as a powerful research tool. In this paper, we present a general overview of the basic operation and functions of AFM applications in biomaterials. The basic operation of AFM is explained in detail with a focus on the real interactions that take place at the nanoscale level during imaging. AFM’s ability to provide the mechanical characterization (force curves) of specific areas at the nanoscale is also explained. The basic models of applied mechanics that are used for processing the data obtained by the force curves are presented. The aim of this paper is to provide university students and young scientists in the fields of biophysics and nanotechnology with a better understanding of AFM. (review)

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

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jingyu; Qian, Yong, E-mail: qianyong86@163.com; Deng, Yonghong; Liu, Di; Li, Hao; Qiu, Xueqing, E-mail: xueqingqiu66@163.com

    2016-12-30

    Graphical abstract: The interactions between lignin and inorganic oxides are quantitatively probed by atomic force microscopy, which is fundamental but beneficial for understanding and optimizing the absorption-dispersion and catalytic degradation processes of lignin. - Highlights: • The interactions between lignin and inorganic oxides are measured using AFM. • The adhesion forces between lignin and metal oxides are larger than that in nonmetal systems. • Hydrogen bond plays an important role in lignin-inorganic oxides system. - Abstract: Understanding the interactions between lignin and inorganic oxides has both fundamental and practical importance in industrial and energy fields. In this work, the specific interactions between alkali lignin (AL) and three inorganic oxide substrates in aqueous environment are quantitatively measured using atomic force microscopy (AFM). The results show that the average adhesion force between AL and metal oxide such as Al{sub 2}O{sub 3} or MgO is nearly two times bigger than that between AL and nonmetal oxide such as SiO{sub 2} due to the electrostatic difference and cation-π interaction. When 83% hydroxyl groups of AL is blocked by acetylation, the adhesion forces between AL and Al{sub 2}O{sub 3}, MgO and SiO{sub 2} decrease 43, 35 and 75% respectively, which indicate hydrogen bonds play an important role between AL and inorganic oxides, especially in AL-silica system.

  6. Motion of guiding center drift atoms in the electric and magnetic field of a Penning trap

    International Nuclear Information System (INIS)

    Kuzmin, S.G.; O'Neil, T.M.

    2005-01-01

    The ApparaTus for High precision Experiment on Neutral Antimatter and antihydrogen TRAP collaborations have produced antihydrogen atoms by recombination in a cryogenic antiproton-positron plasma. This paper discusses the motion of the weakly bound atoms in the electric and magnetic field of the plasma and trap. The effective electric field in the moving frame of the atom polarizes the atom, and then gradients in the field exert a force on the atom. An approximate equation of motion for the atom center of mass is obtained by averaging over the rapid internal dynamics of the atom. The only remnant of the atom internal dynamics that enters this equation is the polarizability for the atom. This coefficient is evaluated for the weakly bound and strongly magnetized (guiding center drift) atoms understood to be produced in the antihydrogen experiments. Application of the approximate equation of motion shows that the atoms can be trapped radially in the large space charge field near the edge of the positron column. Also, an example is presented for which there is full three-dimensional trapping, not just radial trapping. Even untrapped atoms follow curved trajectories, and such trajectories are discussed for the important class of atoms that reach a field ionization diagnostic. Finally, the critical field for ionization is determined as an upper bound on the range of applicability of the theory

  7. Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme

    Energy Technology Data Exchange (ETDEWEB)

    Soares, T. A. [ETH Hoenggerberg Zuerich, Laboratory of Physical Chemistry (Switzerland); Daura, X. [Universitat Autonoma de Barcelona, InstitucioCatalana de Recerca i Estudis Avancats and Institut de Biotecnologia i Biomedicina (Spain); Oostenbrink, C. [ETH Hoenggerberg Zuerich, Laboratory of Physical Chemistry (Switzerland); Smith, L. J. [University of Oxford, Oxford Centre for Molecular Sciences, Central Chemistry Laboratory (United Kingdom); Gunsteren, W. F. van [ETH Hoenggerberg Zuerich, Laboratory of Physical Chemistry (Switzerland)], E-mail: wfvgn@igc.phys.chem.ethz.ch

    2004-12-15

    The quality of molecular dynamics (MD) simulations of proteins depends critically on the biomolecular force field that is used. Such force fields are defined by force-field parameter sets, which are generally determined and improved through calibration of properties of small molecules against experimental or theoretical data. By application to large molecules such as proteins, a new force-field parameter set can be validated. We report two 3.5 ns molecular dynamics simulations of hen egg white lysozyme in water applying the widely used GROMOS force-field parameter set 43A1 and a new set 45A3. The two MD ensembles are evaluated against NMR spectroscopic data NOE atom-atom distance bounds, {sup 3}J{sub NH{alpha}} and {sup 3}J{sub {alpha}}{sub {beta}} coupling constants, and {sup 1}5N relaxation data. It is shown that the two sets reproduce structural properties about equally well. The 45A3 ensemble fulfills the atom-atom distance bounds derived from NMR spectroscopy slightly less well than the 43A1 ensemble, with most of the NOE distance violations in both ensembles involving residues located in loops or flexible regions of the protein. Convergence patterns are very similar in both simulations atom-positional root-mean-square differences (RMSD) with respect to the X-ray and NMR model structures and NOE inter-proton distances converge within 1.0-1.5 ns while backbone {sup 3}J{sub HN{alpha}}-coupling constants and {sup 1}H- {sup 1}5N order parameters take slightly longer, 1.0-2.0 ns. As expected, side-chain {sup 3}J{sub {alpha}}{sub {beta}}-coupling constants and {sup 1}H- {sup 1}5N order parameters do not reach full convergence for all residues in the time period simulated. This is particularly noticeable for side chains which display rare structural transitions. When comparing each simulation trajectory with an older and a newer set of experimental NOE data on lysozyme, it is found that the newer, larger, set of experimental data agrees as well with each of the

  8. Atom Wavelike Nature Solved Mathematically

    Science.gov (United States)

    Sven, Charles

    2010-03-01

    Like N/S poles of a magnet the strong force field surrounding, confining the nucleus exerts an equal force [noted by this author] driving electrons away from the attraction of positively charged protons force fields in nucleus -- the mechanics for wavelike nature of electron. Powerful forces corral closely packed protons within atomic nucleus with a force that is at least a million times stronger than proton's electrical attraction that binds electrons. This then accounts for the ease of electron manipulation in that electron is already pushed away by the very strong atomic N/S force field; allowing electrons to drive photons when I strike a match. Ageless atom's electron requirements, used to drive light/photons or atom bomb, without batteries, must be supplied from a huge, external, super high frequency, super-cooled source, undetected by current technology, one that could exist 14+ billion years without degradation -- filling a limitless space prior to Big Bang. Using only replicable physics, I show how our Universe emanated from that event.

  9. Radical Chemistry and Charge Manipulation with an Atomic Force Microscope

    Science.gov (United States)

    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).

  10. Intermittent contact atomic force microscopy in electrochemical environment

    Energy Technology Data Exchange (ETDEWEB)

    Haering, P; Koetz, R [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Siegenthaler, H [Bern Univ., Bern (Switzerland)

    1997-06-01

    In situ measurements with Atomic Force Microscopy may cause surface modifications due to the tip-surface interactions. As an alternative and less destructive method, Intermittent Contact Atomic Force Microscopy (ICAFM) has been tested in an electrolytic environment. In the ICAFM mode the tip is not constantly in contact with the surface under investigation but is tapping onto the surface with a certain frequency. A commercial Park Scientific Instruments Microscopy has been modified to enable in situ experiment with ICAFM. It was possible to image iridium oxide films with ICAFM in the electrolytic environment without any noticeable surface modifications. (author) 3 figs., 4 refs.

  11. A Cost-Effective Atomic Force Microscope for Undergraduate Control Laboratories

    Science.gov (United States)

    Jones, C. N.; Goncalves, J.

    2010-01-01

    This paper presents a simple, cost-effective and robust atomic force microscope (AFM), which has been purposely designed and built for use as a teaching aid in undergraduate controls labs. The guiding design principle is to have all components be open and visible to the students, so the inner functioning of the microscope has been made clear to…

  12. Mapping Electrostatic Forces Using Higher Harmonics Tapping Mode Atomic Force Microscopy in Liquid

    NARCIS (Netherlands)

    van Noort, S.J.T.; Willemsen, O.H.; van der Werf, Kees; de Grooth, B.G.; Greve, Jan

    1999-01-01

    A simple model of a damped, harmonic oscillator is used to describe the motion of an atomic force microscope cantilever tapping in fluid. By use of experimentally obtained parameters, excellent agreement is found between theory and experimental results. From the model we estimate that the force

  13. Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview.

    Science.gov (United States)

    Riniker, Sereina

    2018-03-26

    In molecular dynamics or Monte Carlo simulations, the interactions between the particles (atoms) in the system are described by a so-called force field. The empirical functional form of classical fixed-charge force fields dates back to 1969 and remains essentially unchanged. In a fixed-charge force field, the polarization is not modeled explicitly, i.e. the effective partial charges do not change depending on conformation and environment. This simplification allows, however, a dramatic reduction in computational cost compared to polarizable force fields and in particular quantum-chemical modeling. The past decades have shown that simulations employing carefully parametrized fixed-charge force fields can provide useful insights into biological and chemical questions. This overview focuses on the four major force-field families, i.e. AMBER, CHARMM, GROMOS, and OPLS, which are based on the same classical functional form and are continuously improved to the present day. The overview is aimed at readers entering the field of (bio)molecular simulations. More experienced users may find the comparison and historical development of the force-field families interesting.

  14. Quantitative measurements of shear displacement using atomic force microscopy

    International Nuclear Information System (INIS)

    Wang, Wenbo; Wu, Weida; Sun, Ying; Zhao, Yonggang

    2016-01-01

    We report a method to quantitatively measure local shear deformation with high sensitivity using atomic force microscopy. The key point is to simultaneously detect both torsional and buckling motions of atomic force microscopy (AFM) cantilevers induced by the lateral piezoelectric response of the sample. This requires the quantitative calibration of torsional and buckling response of AFM. This method is validated by measuring the angular dependence of the in-plane piezoelectric response of a piece of piezoelectric α-quartz. The accurate determination of the amplitude and orientation of the in-plane piezoelectric response, without rotation, would greatly enhance the efficiency of lateral piezoelectric force microscopy.

  15. Probing the Importance of Charge Flux in Force Field Modeling.

    Science.gov (United States)

    Sedghamiz, Elaheh; Nagy, Balazs; Jensen, Frank

    2017-08-08

    We analyze the conformational dependence of atomic charges and molecular dipole moments for a selection of ∼900 conformations of peptide models of the 20 neutral amino acids. Based on a set of reference density functional theory calculations, we partition the changes into effects due to changes in bond distances, bond angles, and torsional angles and into geometry and charge flux contributions. This allows an assessment of the limitations of fixed charge force fields and indications for how to design improved force fields. The torsional degrees of freedom are the main contribution to conformational changes of atomic charges and molecular dipole moments, but indirect effects due to change in bond distances and angles account for ∼25% of the variation. Charge flux effects dominate for changes in bond distances and are also the main component of the variation in bond angles, while they are ∼25% compared to the geometry variations for torsional degrees of freedom. The geometry and charge flux contributions to some extent produce compensating effects.

  16. Forces in electromagnetic field and gravitational field

    OpenAIRE

    Weng, Zihua

    2008-01-01

    The force can be defined from the linear momentum in the gravitational field and electromagnetic field. But this definition can not cover the gradient of energy. In the paper, the force will be defined from the energy and torque in a new way, which involves the gravitational force, electromagnetic force, inertial force, gradient of energy, and some other new force terms etc. One of these new force terms can be used to explain why the solar wind varies velocity along the magnetic force line in...

  17. Algorithms for Reconstruction of Undersampled Atomic Force Microscopy Images Supplementary Material

    DEFF Research Database (Denmark)

    2017-01-01

    Two Jupyter Notebooks showcasing reconstructions of undersampled atomic force microscopy images. The reconstructions were obtained using a variety of interpolation and reconstruction methods.......Two Jupyter Notebooks showcasing reconstructions of undersampled atomic force microscopy images. The reconstructions were obtained using a variety of interpolation and reconstruction methods....

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

    Science.gov (United States)

    Cantrell, John H.; Cantrell, Sean A.

    2010-01-01

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

  19. Brown algal morphogenesis: Atomic Force Microscopy as a tool to study the role of mechanical forces

    Directory of Open Access Journals (Sweden)

    Benoit eTesson

    2014-09-01

    Full Text Available Over the last few years, a growing interest has been directed toward the use of macroalgae as a source of energy, food and molecules for the cosmetic and pharmaceutical industries. Besides this, macroalgal development remains poorly understood compared to other multicellular organisms. Brown algae (Phaeophyceae form a monophyletic lineage of usually large multicellular algae which evolved independently from land plants. In their environment, they are subjected to strong mechanical forces (current, waves and tide, in response to which they modify rapidly and reversibly their morphology. Because of their specific cellular features (cell wall composition, cytoskeleton organization, deciphering how they cope with these forces might help discover new control mechanisms of cell wall softening and cellulose synthesis. Despite the current scarcity in knowledge on brown algal cell wall dynamics and protein composition, we will illustrate, in the light of methods adapted to Ectocarpus siliculosus, to what extent atomic force microscopy can contribute to advance this field of investigation.

  20. Optimization of Easy Atomic Force Microscope (ezAFM) Controls for Semiconductor Nanostructure Profiling

    Science.gov (United States)

    2017-09-01

    ARL-MR-0965 ● SEP 2017 US Army Research Laboratory Optimization of Easy Atomic Force Microscope (ezAFM) Controls for... Optimization of Easy Atomic Force Microscope (ezAFM) Controls for Semiconductor Nanostructure Profiling by Satwik Bisoi Science and...REPORT TYPE Memorandum Report 3. DATES COVERED (From - To) 2017 July 05–2017 August 18 4. TITLE AND SUBTITLE Optimization of Easy Atomic Force

  1. Atomic and free electrons in a strong light field

    CERN Document Server

    Fedorov, Mikhail V

    1997-01-01

    This book presents and describes a series of unusual and striking strong-field phenomena concerning atoms and free electrons. Some of these phenomena are: multiphoton stimulated bremsstrahlung, free-electron lasers, wave-packet physics, above-threshold ionization, and strong-field stabilization in Rydberg atoms. The theoretical foundations and causes of the phenomena are described in detail, with all the approximations and derivations discussed. All the known and relevant experiments are described too, and their results are compared with those of the existing theoretical models.An extensive ge

  2. Athermalization in atomic force microscope based force spectroscopy using matched microstructure coupling.

    Science.gov (United States)

    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.

  3. Modeling Enzymatic Transition States by Force Field Methods

    DEFF Research Database (Denmark)

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

    2009-01-01

    The SEAM method, which models a transition structure as a minimum on the seam of two diabatic surfaces represented by force field functions, has been used to generate 20 transition structures for the decarboxylation of orotidine by the orotidine-5'-monophosphate decarboxylase enzyme. The dependence...... of the TS geometry on the flexibility of the system has been probed by fixing layers of atoms around the active site and using increasingly larger nonbonded cutoffs. The variability over the 20 structures is found to decrease as the system is made more flexible. Relative energies have been calculated...... by various electronic structure methods, where part of the enzyme is represented by a force field description and the effects of the solvent are represented by a continuum model. The relative energies vary by several hundreds of kJ/mol between the transition structures, and tests showed that a large part...

  4. Dispersion Forces

    CERN Document Server

    Buhmann, Stefan Yoshi

    2012-01-01

    In this book, a modern unified theory of dispersion forces on atoms and bodies is presented which covers a broad range of advanced aspects and scenarios. Macroscopic quantum electrodynamics is shown to provide a powerful framework for dispersion forces which allows for discussing general properties like their non-additivity and the relation between microscopic and macroscopic interactions. It is demonstrated how the general results can be used to obtain dispersion forces on atoms in the presence of bodies of various shapes and materials. Starting with a brief recapitulation of volume I, this volume II deals especially with bodies of irregular shapes, universal scaling laws, dynamical forces on excited atoms, enhanced forces in cavity quantum electrodynamics, non-equilibrium forces in thermal environments and quantum friction. The book gives both the specialist and those new to the field a thorough overview over recent results in the field. It provides a toolbox for studying dispersion forces in various contex...

  5. Minimizing pulling geometry errors in atomic force microscope single molecule force spectroscopy.

    Science.gov (United States)

    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.

  6. z calibration of the atomic force microscope by means of a pyramidal tip

    DEFF Research Database (Denmark)

    Jensen, Flemming

    1993-01-01

    A new method for imaging the probe tip of an atomic force microscope cantilever by the atomic force microscope itself (self-imaging) is presented. The self-imaging is accomplished by scanning the probe tip across a sharper tip on the surface. By using a pyramidal probe tip with a very well......-defined aspect ratio, this technique provides an excellent z-calibration standard for the atomic force microscope....

  7. Force, current and field effects in single atom manipulation

    NARCIS (Netherlands)

    Braun, K.-F.; Hla, S.; Pertaya, N.; Soe, W.H.; Flipse, C.F.J.; Rieder, K.

    2003-01-01

    We present a detailed investigation of the manipulation of Ag and Au atoms with a STM tip on the Ag(111) surface at 5K. The interpretation of the feed-back loop signal gives a precise picture of the movement of the atom during manipulation. The threshold tunnelling resistance and tip-height to move

  8. Effect of contact stiffness on wedge calibration of lateral force in atomic force microscopy

    International Nuclear Information System (INIS)

    Wang Fei; Zhao Xuezeng

    2007-01-01

    Quantitative friction measurement of nanomaterials in atomic force microscope requires accurate calibration method for lateral force. The effect of contact stiffness on lateral force calibration of atomic force microscope is discussed in detail and an improved calibration method is presented. The calibration factor derived from the original method increased with the applied normal load, which indicates that separate calibration should be required for every given applied normal load to keep the accuracy of friction measurement. We improve the original method by introducing the contact factor, which is derived from the contact stiffness between the tip and the sample, to the calculation of calibration factors. The improved method makes the calculation of calibration factors under different applied normal loads possible without repeating the calibration procedure. Comparative experiments on a silicon wafer have been done by both the two methods to validate the method in this article

  9. Evolution Properties of Atomic Fidelity in the Combined Multi-Atom-Cavity Field System

    International Nuclear Information System (INIS)

    Wang Ju-Xia; Zhang Xiao-Juan; Zhang Xiu-Xing

    2015-01-01

    The atom fidelity is investigated in a system consisting of Mtwo-level atoms and M single-mode fields by use of complete quantum theory and numerical evaluation method. The influences of various system parameters on the evolution of atomic fidelity are studied. The results show that the atomic fidelity evolves in a Rabi oscillation manner. The oscillation frequency is mainly modulated by the coupling strength between atoms and light field, the atomic transition probabilities and the average photon numbers. Other factors hardly impact on the atomic fidelity. The present results may provide a useful approach to the maintenance of the atomic fidelity in the atom cavity field systems. (paper)

  10. Atomic excitation and recombination in external fields

    International Nuclear Information System (INIS)

    Nayfeh, M.H.; Clark, C.W.

    1985-01-01

    This volume offers a timely look at Rydberg states of atoms in external fields and dielectronic recombination. Each topic provides authoritative coverage, presents a fresh account of a flourishing field of current atomic physics and introduces new opportunities for discovery and development. Topics considered include electron-atom scattering in external fields; observations of regular and irregular motion as exemplified by the quadratic zeeman effect and other systems; Rydberg atoms in external fields and the Coulomb geometry; crossed-field effects in the absorption spectrum of lithium in a magnetic field; precise studies of static electric field ionization; widths and shapes of stark resonances in sodium above the saddle point; studies of electric field effects and barium autoionizing resonances; autoionization and dielectronic recombination in plasma electric microfields; dielectronic recombination measurements on multicharged ions; merged beam studies of dielectronic recombination; Rydberg atoms and dielectronic recombination in astrophysics; and observations on dielectronic recombination

  11. Digital phase-shifting atomic force microscope Moire method

    International Nuclear Information System (INIS)

    Liu Chiaming; Chen Lienwen

    2005-01-01

    In this study, the digital atomic force microscope (AFM) Moire method with phase-shifting technology is established to measure the in-plane displacement and strain fields. The Moire pattern is generated by the interference between the specimen grating and the virtual reference grating formed by digital image processes. The overlapped image is filtered by two-dimensional wavelet transformation to obtain the clear interference Moire patterns. The four-step phase-shifting method is realized by translating the phase of the virtual reference grating from 0 to 2π. The principle of the digital AFM Moire method and the phase-shifting technology are described in detail. Experimental results show that this method is convenient to use and efficient in realizing the microscale measurement

  12. Modeling noncontact atomic force microscopy resolution on corrugated surfaces

    Directory of Open Access Journals (Sweden)

    Kristen M. Burson

    2012-03-01

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

  13. Resolving amorphous solid-liquid interfaces by atomic force microscopy

    International Nuclear Information System (INIS)

    Burson, Kristen M.; Gura, Leonard; Kell, Burkhard; Büchner, Christin; Lewandowski, Adrian L.; Heyde, Markus; Freund, Hans-Joachim

    2016-01-01

    Recent advancements in liquid atomic force microscopy make it an ideal technique for probing the structure of solid-liquid interfaces. Here, we present a structural study of a two-dimensional amorphous silica bilayer immersed in an aqueous solution utilizing liquid atomic force microscopy with sub-nanometer resolution. Structures show good agreement with atomically resolved ultra-high vacuum scanning tunneling microscopy images obtained on the same sample system, owing to the structural stability of the silica bilayer and the imaging clarity from the two-dimensional sample system. Pair distance histograms of ring center positions are utilized to develop quantitative metrics for structural comparison, and the physical origin of pair distance histogram peaks is addressed by direct assessment of real space structures.

  14. Atomic force microscopy and confocal laser scanning microscopy on the cytoskeleton of permeabilised and embedded cells

    International Nuclear Information System (INIS)

    Meller, Karl; Theiss, Carsten

    2006-01-01

    We describe a technical method of cell permeabilisation and embedding to study the organisation and distribution of intracellular proteins with aid of atomic force microscopy and confocal laser scanning microscopy in identical areas. While confocal laser scanning microscopy is useful for the identification of certain proteins subsequent labelling with markers or antibodies, atomic force microscopy allows the observation of macromolecular structures in fixed and living cells. To demonstrate the field of application of this preparatory technique, cells were permeabilised, fixed, and the actin cytoskeleton was stained with phalloidin-rhodamine. Confocal laser scanning microscopy was used to show the organisation of these microfilaments, e.g. geodesic dome structures. Thereafter, cells were embedded in Durcupan water-soluble resin, followed by UV-polymerisation of resin at 4 o C. This procedure allowed intracellular visualisation of the cell nucleus or cytoskeletal elements by atomic force microscopy, for instance to analyse the globular organisation of actin filaments. Therefore, this method offers a great potential to combine both microscopy techniques in order to understand and interpret intracellular protein relations, for example, the biochemical and morphological interaction of the cytoskeleton

  15. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer’s peptides

    Energy Technology Data Exchange (ETDEWEB)

    Tran, Thanh Thuy; Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr; Derreumaux, Philippe, E-mail: philippe.derreumaux@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)

    2016-05-28

    Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ{sub 16−22} and Aβ{sub 37−42} of the full length Aβ{sub 1−42} Alzheimer’s peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ{sub 16−22} dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ{sub 16−22} and the dimer and trimer of Aβ{sub 37−42}. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ{sub 16−22} decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ{sub 37−42} decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.

  16. Production and detection of atomic hexadecapole at Earth's magnetic field.

    Science.gov (United States)

    Acosta, V M; Auzinsh, M; Gawlik, W; Grisins, P; Higbie, J M; Jackson Kimball, D F; Krzemien, L; Ledbetter, M P; Pustelny, S; Rochester, S M; Yashchuk, V V; Budker, D

    2008-07-21

    Optical magnetometers measure magnetic fields with extremely high precision and without cryogenics. However, at geomagnetic fields, important for applications from landmine removal to archaeology, they suffer from nonlinear Zeeman splitting, leading to systematic dependence on sensor orientation. We present experimental results on a method of eliminating this systematic error, using the hexadecapole atomic polarization moment. In particular, we demonstrate selective production of the atomic hexadecapole moment at Earth's magnetic field and verify its immunity to nonlinear Zeeman splitting. This technique promises to eliminate directional errors in all-optical atomic magnetometers, potentially improving their measurement accuracy by several orders of magnitude.

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

    Science.gov (United States)

    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.

  18. Casimir Forces and Quantum Friction from Ginzburg Radiation in Atomic Bose-Einstein Condensates.

    Science.gov (United States)

    Marino, Jamir; Recati, Alessio; Carusotto, Iacopo

    2017-01-27

    We theoretically propose an experimentally viable scheme to use an impurity atom in an atomic Bose-Einstein condensate, in order to realize condensed-matter analogs of quantum vacuum effects. In a suitable atomic level configuration, the collisional interaction between the impurity atom and the density fluctuations in the condensate can be tailored to closely reproduce the electric-dipole coupling of quantum electrodynamics. By virtue of this analogy, we recover and extend the paradigm of electromagnetic vacuum forces to the domain of cold atoms, showing in particular the emergence, at supersonic atomic speeds, of a novel power-law scaling of the Casimir force felt by the atomic impurity, as well as the occurrence of a quantum frictional force, accompanied by the Ginzburg emission of Bogoliubov quanta. Observable consequences of these quantum vacuum effects in realistic spectroscopic experiments are discussed.

  19. Imaging stability in force-feedback high-speed atomic force microscopy

    International Nuclear Information System (INIS)

    Kim, Byung I.; Boehm, Ryan D.

    2013-01-01

    We studied the stability of force-feedback high-speed atomic force microscopy (HSAFM) by imaging soft, hard, and biological sample surfaces at various applied forces. The HSAFM images showed sudden topographic variations of streaky fringes with a negative applied force when collected on a soft hydrocarbon film grown on a grating sample, whereas they showed stable topographic features with positive applied forces. The instability of HSAFM images with the negative applied force was explained by the transition between contact and noncontact regimes in the force–distance curve. When the grating surface was cleaned, and thus hydrophilic by removing the hydrocarbon film, enhanced imaging stability was observed at both positive and negative applied forces. The higher adhesive interaction between the tip and the surface explains the improved imaging stability. The effects of imaging rate on the imaging stability were tested on an even softer adhesive Escherichia coli biofilm deposited onto the grating structure. The biofilm and planktonic cell structures in HSAFM images were reproducible within the force deviation less than ∼0.5 nN at the imaging rate up to 0.2 s per frame, suggesting that the force-feedback HSAFM was stable for various imaging speeds in imaging softer adhesive biological samples. - Highlights: ► We investigated the imaging stability of force-feedback HSAFM. ► Stable–unstable imaging transitions rely on applied force and sample hydrophilicity. ► The stable–unstable transitions are found to be independent of imaging rate

  20. Single molecule atomic force microscopy and force spectroscopy of chitosan.

    Science.gov (United States)

    Kocun, Marta; Grandbois, Michel; Cuccia, Louis A

    2011-02-01

    Atomic force microscopy (AFM) and AFM-based force spectroscopy was used to study the desorption of individual chitosan polymer chains from substrates with varying chemical composition. AFM images of chitosan adsorbed onto a flat mica substrate show elongated single strands or aggregated bundles. The aggregated state of the polymer is consistent with the high level of flexibility and mobility expected for a highly positively charged polymer strand. Conversely, the visualization of elongated strands indicated the presence of stabilizing interactions with the substrate. Surfaces with varying chemical composition (glass, self-assembled monolayer of mercaptoundecanoic acid/decanethiol and polytetrafluoroethylene (PTFE)) were probed with chitosan modified AFM tips and the corresponding desorption energies, calculated from plateau-like features, were attributed to the desorption of individual polymer strands. Desorption energies of 2.0±0.3×10(-20)J, 1.8±0.3×10(-20)J and 3.5±0.3×10(-20)J were obtained for glass, SAM of mercaptoundecanoic/dodecanethiol and PTFE, respectively. These single molecule level results can be used as a basis for investigating chitosan and chitosan-based materials for biomaterial applications. Copyright © 2010 Elsevier B.V. All rights reserved.

  1. The development of the spatially correlated adjustment wavelet filter for atomic force microscopy data.

    Science.gov (United States)

    Sikora, Andrzej; Rodak, Aleksander; Unold, Olgierd; Klapetek, Petr

    2016-12-01

    In this paper a novel approach for the practical utilization of the 2D wavelet filter in terms of the artifacts removal from atomic force microscopy measurements results is presented. The utilization of additional data such as summary photodiode signal map is implemented in terms of the identification of the areas requiring the data processing, filtering settings optimization and the verification of the process performance. Such an approach allows to perform the filtering parameters adjustment by average user, while the straightforward method requires an expertise in this field. The procedure was developed as the function of the Gwyddion software. The examples of filtering the phase imaging and Electrostatic Force Microscopy measurement result are presented. As the wavelet filtering feature may remove a local artifacts, its superior efficiency over similar approach with 2D Fast Fourier Transformate based filter (2D FFT) can be noticed. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Probing new intra-atomic force with isotope shifts

    Energy Technology Data Exchange (ETDEWEB)

    Mikami, Kyoko; Tanaka, Minoru [Osaka University, Department of Physics, Graduate School of Science, Toyonaka, Osaka (Japan); Yamamoto, Yasuhiro [Yonsei University, Department of Physics and IPAP, Seoul (Korea, Republic of)

    2017-12-15

    In the development of atomic clocks, some atomic transition frequencies are measured with remarkable precision. These measured spectra may include the effects of a new force mediated by a weakly interacting boson. Such effects might be distilled out from possible violation of a linear relation in isotope shifts between two transitions, as known as King's linearity, with relatively suppressed theoretical uncertainties. We discuss the experimental sensitivity to a new force in the test of the linearity as well as the linearity violation owing to higher-order effects within the Standard Model. The sensitivity to new physics is limited by such effects. We have found that, for Yb{sup +}, the higher-order effect is in the reach of future experiments. The sensitivity to a heavy mediator is also discussed. It is analytically clarified that the sensitivity becomes weaker than that in the literature. Our numerical results of the sensitivity are compared with other weak force search experiments. (orig.)

  3. Identification and ultrastructural imaging of photodynamic therapy-induced microfilaments by atomic force microscopy

    International Nuclear Information System (INIS)

    Jung, Se-Hui; Park, Jin-Young; Yoo, Je-Ok; Shin, Incheol; Kim, Young-Myeong; Ha, Kwon-Soo

    2009-01-01

    Atomic force microscopy (AFM) is an emerging technique for imaging biological samples at subnanometer resolution; however, the method is not widely used for cell imaging because it is limited to analysis of surface topology. In this study, we demonstrate identification and ultrastructural imaging of microfilaments using new approaches based on AFM. Photodynamic therapy (PDT) with a new chlorin-based photosensitizer DH-II-24 induced cell shrinkage, membrane blebbing, and reorganization of cytoskeletons in bladder cancer J82 cells. We investigated cytoskeletal changes using confocal microscopy and atomic force microscopy. Extracellular filaments formed by PDT were analyzed with a tandem imaging approach based on confocal microscopy and atomic force microscopy. Ultrathin filaments that were not visible by confocal microscopy were identified as microfilaments by on-stage labeling/imaging using atomic force microscopy. Furthermore, ultrastructural imaging revealed that these microfilaments had a stranded helical structure. Thus, these new approaches were useful for ultrastructural imaging of microfilaments at the molecular level, and, moreover, they may help to overcome the current limitations of fluorescence-based microscopy and atomic force microscopy in cell imaging.

  4. Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations.

    Science.gov (United States)

    Pavlova, Anna; Parks, Jerry M; Gumbart, James C

    2018-02-13

    Corrinoid cofactors such as cobalamin are used by many enzymes and are essential for most living organisms. Therefore, there is broad interest in investigating cobalamin-protein interactions with molecular dynamics simulations. Previously developed parameters for cobalamins are based mainly on crystal structure data. Here, we report CHARMM-compatible force field parameters for several corrinoids developed from quantum mechanical calculations. We provide parameters for corrinoids in three oxidation states, Co 3+ , Co 2+ , and Co 1+ , and with various axial ligands. Lennard-Jones parameters for the cobalt center in the Co(II) and Co(I) states were optimized using a helium atom probe, and partial atomic charges were obtained with a combination of natural population analysis (NPA) and restrained electrostatic potential (RESP) fitting approaches. The Force Field Toolkit was used to optimize all bonded terms. The resulting parameters, determined solely from calculations of cobalamin alone or in water, were then validated by assessing their agreement with density functional theory geometries and by analyzing molecular dynamics simulation trajectories of several corrinoid proteins for which X-ray crystal structures are available. In each case, we obtained excellent agreement with the reference data. In comparison to previous CHARMM-compatible parameters for cobalamin, we observe a better agreement for the fold angle and lower RMSD in the cobalamin binding site. The approach described here is readily adaptable for developing CHARMM-compatible force-field parameters for other corrinoids or large biomolecules.

  5. Stacking it up: Exploring the limits of ultra-high resolution atomic force microscopy

    NARCIS (Netherlands)

    van der Heijden, N.J.

    2017-01-01

    Atomic force microscopy (AFM) is a technique wherein an atomically sharp needle raster scans across a surface, detecting forces between it and the sample. In state-of-the-art AFM experiments the measured forces are typically on the order of pico-Newtons, and the lateral resolution is on the order of

  6. Spectroscopy and atomic force microscopy of biomass.

    Science.gov (United States)

    Tetard, L; Passian, A; Farahi, R H; Kalluri, U C; Davison, B H; Thundat, T

    2010-05-01

    Scanning probe microscopy has emerged as a powerful approach to a broader understanding of the molecular architecture of cell walls, which may shed light on the challenge of efficient cellulosic ethanol production. We have obtained preliminary images of both Populus and switchgrass samples using atomic force microscopy (AFM). The results show distinctive features that are shared by switchgrass and Populus. These features may be attributable to the lignocellulosic cell wall composition, as the collected images exhibit the characteristic macromolecular globule structures attributable to the lignocellulosic systems. Using both AFM and a single case of mode synthesizing atomic force microscopy (MSAFM) to characterize Populus, we obtained images that clearly show the cell wall structure. The results are of importance in providing a better understanding of the characteristic features of both mature cells as well as developing plant cells. In addition, we present spectroscopic investigation of the same samples.

  7. A verification of quantum field theory – measurement of Casimir force

    Indian Academy of Sciences (India)

    journal of. Feb. & Mar. 2001 physics pp. 239–243. A verification of quantum field theory ... minum coated a sphere and flat plate using an atomic force microscope. ... where R is the radius of curvature of the spherical surface. The finite .... sured by AFM) of 60% Au/40% Pd, to form a nonreactive and conductive top layer. For.

  8. Improvement of a force field to model the edges of clay particles

    International Nuclear Information System (INIS)

    Pouvreau, Maxime

    2016-01-01

    The CLAYFF force field is widely used to model the interfaces of clay minerals - and related layered materials - with an aqueous phase. In the simulations, clay particles are typically represented by semi-infinite layers, i.e. only surfaces parallel to the layer plane (basal surfaces) are considered. This simplification is acceptable to a certain extent, but clay layers are really nano sized and terminated by lateral surfaces or edges. These surfaces can not only adsorb solvated species but are also subject to proton transfers, and all physico-chemical processes related to the aqueous phase acidity predominantly occur at the edges. By adding to the CLAYFF force field a Metal-O-H angle bending term whose parameters are correctly adjusted, the simulations of edge interfaces become possible.The parameters of Al-O-H and Mg-O-H terms were obtained from DFT calculations on bulk, basal surface and edge structural models of gibbsite Al(OH) 3 and brucite Mg(OH) 2 , whose layers can be considered as the backbones of clay minerals and related materials. In addition, the Si-O-H term was parametrized from an edge model of kaolinite Al 2 Si 2 O 5 (OH) 4 . Molecular dynamics simulations based on DFT and on CLAYFF with and without Metal-O-H term were performed. The modified force field clearly improves the description of hydroxylated surfaces: the orientation and the vibrational dynamics of the hydroxyl groups, the hydrogen bonding, and the coordination of metal atoms belonging to the edge are all closer to reality [fr

  9. Investigating biomolecular recognition at the cell surface using atomic force microscopy.

    Science.gov (United States)

    Wang, Congzhou; Yadavalli, Vamsi K

    2014-05-01

    Probing the interaction forces that drive biomolecular recognition on cell surfaces is essential for understanding diverse biological processes. Force spectroscopy has been a widely used dynamic analytical technique, allowing measurement of such interactions at the molecular and cellular level. The capabilities of working under near physiological environments, combined with excellent force and lateral resolution make atomic force microscopy (AFM)-based force spectroscopy a powerful approach to measure biomolecular interaction forces not only on non-biological substrates, but also on soft, dynamic cell surfaces. Over the last few years, AFM-based force spectroscopy has provided biophysical insight into how biomolecules on cell surfaces interact with each other and induce relevant biological processes. In this review, we focus on describing the technique of force spectroscopy using the AFM, specifically in the context of probing cell surfaces. We summarize recent progress in understanding the recognition and interactions between macromolecules that may be found at cell surfaces from a force spectroscopy perspective. We further discuss the challenges and future prospects of the application of this versatile technique. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. FEATURES OF MEASURING IN LIQUID MEDIA BY ATOMIC FORCE MICROSCOPY

    Directory of Open Access Journals (Sweden)

    Mikhail V. Zhukov

    2016-11-01

    Full Text Available Subject of Research.The paper presents results of experimental study of measurement features in liquids by atomic force microscope to identify the best modes and buffered media as well as to find possible image artifacts and ways of their elimination. Method. The atomic force microscope Ntegra Aura (NT-MDT, Russia with standard prism probe holder and liquid cell was used to carry out measurements in liquids. The calibration lattice TGQ1 (NT-MDT, Russia was chosen as investigated structure with a fixed shape and height. Main Results. The research of probe functioning in specific pH liquids (distilled water, PBS - sodium phosphate buffer, Na2HPO4 - borate buffer, NaOH 0.1 M, NaOH 0.5 M was carried out in contact and semi-contact modes. The optimal operating conditions and the best media for the liquid measurements were found. Comparison of atomic force microscopy data with the results of lattice study by scanning electron microscopy was performed. The features of the feedback system response in the «probe-surface» interaction were considered by the approach/retraction curves in the different environments. An artifact of image inversion was analyzed and recommendation for its elimination was provided. Practical Relevance. These studies reveal the possibility of fine alignment of research method for objects of organic and inorganic nature by atomic force microscopy in liquid media.

  11. Probing stem cell differentiation using atomic force microscopy

    International Nuclear Information System (INIS)

    Liang, Xiaobin; Shi, Xuetao; Ostrovidov, Serge; Wu, Hongkai; Nakajima, Ken

    2016-01-01

    Graphical abstract: - Highlights: • Atomic force microscopy (AFM) was developed to probe stem cell differentiation. • The mechanical properties of stem cells and their ECMs can be used to clearly distinguish specific stem cell-differentiated lineages. • AFM is a facile and useful tool for monitoring stem cell differentiation in a non-invasive manner. - Abstract: A real-time method using atomic force microscopy (AFM) was developed to probe stem cell differentiation by measuring the mechanical properties of cells and the extracellular matrix (ECM). The mechanical properties of stem cells and their ECMs can be used to clearly distinguish specific stem cell-differentiated lineages. It is clear that AFM is a facile and useful tool for monitoring the differentiation of stem cells in a non-invasive manner.

  12. Probing stem cell differentiation using atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Xiaobin [Graduate School of Science and Engineering, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-ku, Tokyo 152-8550 (Japan); Shi, Xuetao, E-mail: mrshixuetao@gmail.com [School of Materials Science and Engineering, South China University of Technology, Guangzhou 510641 (China); Ostrovidov, Serge [WPI-Advanced Institute for Materials Research, Tohoku University, Sendai (Japan); Wu, Hongkai, E-mail: chhkwu@ust.hk [Department of Chemistry & Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong (China); Nakajima, Ken [Graduate School of Science and Engineering, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-ku, Tokyo 152-8550 (Japan)

    2016-03-15

    Graphical abstract: - Highlights: • Atomic force microscopy (AFM) was developed to probe stem cell differentiation. • The mechanical properties of stem cells and their ECMs can be used to clearly distinguish specific stem cell-differentiated lineages. • AFM is a facile and useful tool for monitoring stem cell differentiation in a non-invasive manner. - Abstract: A real-time method using atomic force microscopy (AFM) was developed to probe stem cell differentiation by measuring the mechanical properties of cells and the extracellular matrix (ECM). The mechanical properties of stem cells and their ECMs can be used to clearly distinguish specific stem cell-differentiated lineages. It is clear that AFM is a facile and useful tool for monitoring the differentiation of stem cells in a non-invasive manner.

  13. ATK-ForceField: a new generation molecular dynamics software package

    Science.gov (United States)

    Schneider, Julian; Hamaekers, Jan; Chill, Samuel T.; Smidstrup, Søren; Bulin, Johannes; Thesen, Ralph; Blom, Anders; Stokbro, Kurt

    2017-12-01

    ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal.

  14. Atomic Interference in Standing Wave Fields

    National Research Council Canada - National Science Library

    Berman, Paul

    2001-01-01

    ... on (i) a conical lens that can he used to focus atoms to a single spot, (ii) a multi-color field geometry that can be used to produce high-harmonic, sinusoidal, spatial matter gratings in a single atomic-field interaction zone, (iii...

  15. Steering neutral atoms in strong laser fields

    International Nuclear Information System (INIS)

    Eilzer, S; Eichmann, U

    2014-01-01

    The seminal strong-field tunnelling theory introduced by L V Keldysh plays a pivotal role. It has shaped our understanding of atomic strong-field processes, where it represents the first step in complex ionisation dynamics and provides reliable tunnelling rates. Tunnelling rates, however, cannot be necessarily equated with ionisation rates. Taking into account the electron dynamics in the Coulomb potential following the tunnelling process, the process of frustrated tunnelling ionisation has been found to lead to excited Rydberg atoms. Here, we excite He atoms in the strong-field tunnelling regime into Rydberg states. A high percentage of these Rydberg atoms survive in high intensity laser fields. We exploit this fact together with their high polarisability to kinematically manipulate the Rydberg atoms with a second elliptically polarised focused strong laser field. By varying the spatial overlap of the two laser foci, we are able to selectively control the deflection of the Rydberg atoms. The results of semi-classical calculations, which are based on the frustrated tunnelling model and on the ponderomotive acceleration, are in accord with our experimental data. (paper)

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  18. Tapping mode atomic force microscopy in liquid

    NARCIS (Netherlands)

    Putman, Constant A.J.; Putman, C.A.J.; van der Werf, Kees; de Grooth, B.G.; van Hulst, N.F.; Greve, Jan

    1994-01-01

    We show that standard silicon nitride cantilevers can be used for tapping mode atomic force microscopy (AFM) in air, provided that the energy of the oscillating cantilever is sufficiently high to overcome the adhesion of the water layer. The same cantilevers are successfully used for tapping mode

  19. Microparticle adhesion studies by atomic force microscopy

    NARCIS (Netherlands)

    Segeren, L.H.G.J.; Siebum, B.; Karssenberg, F.G.; Berg, van den J.W.A.; Vancso, G.J.

    2002-01-01

    Atomic force microscopy (AFM) is one of the most flexible and simple techniques for probing surface interactions. This article reviews AFM studies on particle adhesion. Special attention is paid to the characterization of roughness and its effect on adhesion. This is of importance when comparing the

  20. Atomic Force Microscopy: A Powerful Tool to Address Scaffold Design in Tissue Engineering.

    Science.gov (United States)

    Marrese, Marica; Guarino, Vincenzo; Ambrosio, Luigi

    2017-02-13

    Functional polymers currently represent a basic component of a large range of biological and biomedical applications including molecular release, tissue engineering, bio-sensing and medical imaging. Advancements in these fields are driven by the use of a wide set of biodegradable polymers with controlled physical and bio-interactive properties. In this context, microscopy techniques such as Atomic Force Microscopy (AFM) are emerging as fundamental tools to deeply investigate morphology and structural properties at micro and sub-micrometric scale, in order to evaluate the in time relationship between physicochemical properties of biomaterials and biological response. In particular, AFM is not only a mere tool for screening surface topography, but may offer a significant contribution to understand surface and interface properties, thus concurring to the optimization of biomaterials performance, processes, physical and chemical properties at the micro and nanoscale. This is possible by capitalizing the recent discoveries in nanotechnologies applied to soft matter such as atomic force spectroscopy to measure surface forces through force curves. By tip-sample local interactions, several information can be collected such as elasticity, viscoelasticity, surface charge densities and wettability. This paper overviews recent developments in AFM technology and imaging techniques by remarking differences in operational modes, the implementation of advanced tools and their current application in biomaterials science, in terms of characterization of polymeric devices in different forms (i.e., fibres, films or particles).

  1. Atomic Force Microscopy: A Powerful Tool to Address Scaffold Design in Tissue Engineering

    Directory of Open Access Journals (Sweden)

    Marica Marrese

    2017-02-01

    Full Text Available Functional polymers currently represent a basic component of a large range of biological and biomedical applications including molecular release, tissue engineering, bio-sensing and medical imaging. Advancements in these fields are driven by the use of a wide set of biodegradable polymers with controlled physical and bio-interactive properties. In this context, microscopy techniques such as Atomic Force Microscopy (AFM are emerging as fundamental tools to deeply investigate morphology and structural properties at micro and sub-micrometric scale, in order to evaluate the in time relationship between physicochemical properties of biomaterials and biological response. In particular, AFM is not only a mere tool for screening surface topography, but may offer a significant contribution to understand surface and interface properties, thus concurring to the optimization of biomaterials performance, processes, physical and chemical properties at the micro and nanoscale. This is possible by capitalizing the recent discoveries in nanotechnologies applied to soft matter such as atomic force spectroscopy to measure surface forces through force curves. By tip-sample local interactions, several information can be collected such as elasticity, viscoelasticity, surface charge densities and wettability. This paper overviews recent developments in AFM technology and imaging techniques by remarking differences in operational modes, the implementation of advanced tools and their current application in biomaterials science, in terms of characterization of polymeric devices in different forms (i.e., fibres, films or particles.

  2. Resonance properties of a three-level atom with quantized field modes

    International Nuclear Information System (INIS)

    Yoo, H.I.

    1984-01-01

    A system of one three-level atom and one or two quantized electro-magnetic field modes coupled to each other by the dipole interaction, with the rotating wave approximation is studied. All three atomic configurations, i.e., cascade Lambda- and V-types, are treated simultaneously. The system is treated as closed, i.e., no interaction with the external radiation field modes, to reveal the internal structures and symmetries in the system. The general dynamics of the system are investigated under several distinct initial conditions and their similarities and differences with the dynamics of the Jaynes-Cummings model are revealed. Also investigated is the possibility of so-called coherent trapping of the atom in the quantized field modes in a resonator. An atomic state of coherent trapping exists only for limited cases, and it generally requires the field to be in some special states, depending on the system. The discussion of coherent trapping is extended into a system of M identical three-level atoms. The stability of a coherent-trapping state when fluorescence can take place is discussed. The distinction between a system with resonator field modes and one with ideal laser modes is made clear, and the atomic relaxation to the coherent-trapping atomic state when a Lambda-type atom is irradiated by two ideal laser beams is studied. The experimental prospects to observe the collapse-revival phenomena in the atomic occupation probabilities, which is characteristic of a system with quantized resonator field modes is discussed

  3. Pulsed-laser atom-probe field-ion microscopy

    International Nuclear Information System (INIS)

    Kellogg, G.L.; Tsong, T.T.

    1980-01-01

    A time-of-flight atom-probe field-ion microscope has been developed which uses nanosecond laser pulses to field evaporate surface species. The ability to operate an atom-probe without using high-voltage pulses is advantageous for several reasons. The spread in energy arising from the desorption of surface species prior to the voltage pulse attaining its maximum amplitude is eliminated, resulting in increased mass resolution. Semiconductor and insulator samples, for which the electrical resistivity is too high to transmit a short-duration voltage pulse, can be examined using pulsed-laser assisted field desorption. Since the electric field at the surface can be significantly smaller, the dissociation of molecular adsorbates by the field can be reduced or eliminated, permitting well-defined studies of surface chemical reactions. In addition to atom-probe operation, pulsed-laser heating of field emitters can be used to study surface diffusion of adatoms and vacancies over a wide range of temperatures. Examples demonstrating each of these advantages are presented, including the first pulsed-laser atom-probe (PLAP) mass spectra for both metals (W, Mo, Rh) and semiconductors (Si). Molecular hydrogen, which desorbs exclusively as atomic hydrogen in the conventional atom probe, is shown to desorb undissociatively in the PLAP. Field-ion microscope observations of the diffusion and dissociation of atomic clusters, the migration of adatoms, and the formation of vacancies resulting from heating with a 7-ns laser pulse are also presented

  4. Systematic implicit solvent coarse-graining of bilayer membranes: lipid and phase transferability of the force field

    Energy Technology Data Exchange (ETDEWEB)

    Wang Zunjing; Deserno, Markus, E-mail: zwang@cmu.ed, E-mail: deserno@andrew.cmu.ed [Department of Physics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213 (United States)

    2010-09-15

    We study the lipid and phase transferability of our recently developed systematically coarse-grained solvent-free membrane model. The force field was explicitly parameterized to describe a fluid 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer at 310 K with correct structure and area per lipid, while gaining at least three orders of magnitude in computational efficiency (see Wang and Deserno 2010 J. Phys. Chem. B 114 11207-20). Here, we show that exchanging CG tails, without any subsequent re-parameterization, creates reliable models of 1,2-dioleoylphosphatidylcholine (DOPC) and 1,2-dipalmitoylphosphatidylcholine (DPPC) lipids in terms of structure and area per lipid. Furthermore, all CG lipids undergo a liquid-gel transition upon cooling, with characteristics like those observed in experiments and all-atom simulations during phase transformation. These studies suggest a promising transferability of our force field parameters to different lipid species and thermodynamic state points, properties that are a prerequisite for even more complex systems, such as mixtures.

  5. Systematic implicit solvent coarse-graining of bilayer membranes: lipid and phase transferability of the force field

    International Nuclear Information System (INIS)

    Wang Zunjing; Deserno, Markus

    2010-01-01

    We study the lipid and phase transferability of our recently developed systematically coarse-grained solvent-free membrane model. The force field was explicitly parameterized to describe a fluid 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer at 310 K with correct structure and area per lipid, while gaining at least three orders of magnitude in computational efficiency (see Wang and Deserno 2010 J. Phys. Chem. B 114 11207-20). Here, we show that exchanging CG tails, without any subsequent re-parameterization, creates reliable models of 1,2-dioleoylphosphatidylcholine (DOPC) and 1,2-dipalmitoylphosphatidylcholine (DPPC) lipids in terms of structure and area per lipid. Furthermore, all CG lipids undergo a liquid-gel transition upon cooling, with characteristics like those observed in experiments and all-atom simulations during phase transformation. These studies suggest a promising transferability of our force field parameters to different lipid species and thermodynamic state points, properties that are a prerequisite for even more complex systems, such as mixtures.

  6. Capillary force between wetted nanometric contacts and its application to atomic force microscopy.

    Science.gov (United States)

    Crassous, Jérôme; Ciccotti, Matteo; Charlaix, Elisabeth

    2011-04-05

    We extend to the case of perfect wetting the exact calculation of Orr et al. (J. Fluid. Mech. 1975, 67, 723) for a pendular ring connecting two dry surfaces. We derive an approximate analytical expression for the capillary force between two highly curved surfaces covered by a wetting liquid film. The domain of validity of this expression is assessed and extended by a custom-made numerical simulation based on the full exact mathematical description. In the case of attractive liquid-solid van der Waals interactions, the capillary force increases monotonically with decreasing vapor pressure up to several times its saturation value. This accurate description of the capillary force makes it possible to estimate the adhesion force between wet nanoparticles; it can also be used to quantitatively interpret pull-off forces measured by atomic force microscopy.

  7. Atomic and Free Electrons in a Strong Light Field

    International Nuclear Information System (INIS)

    Fedorov, Mikhail V.

    1998-02-01

    This book presents and describes a series of unusual and striking strong-field phenomena concerning atoms and free electrons. Some of these phenomena are: multiphoton stimulated Bremsstrahlung, free-electron lasers, ave-packet physics, above-threshold ionization, and strong-field stabilization in Rydberg atoms. The theoretical foundations and causes of the phenomena are described in detail, with all the approximations and derivations discussed. All the known and relevant experiments are described oo, and their results are compared with those of the existing theoretical models. An extensive general theoretical introduction gives a good basis for subsequent parts of the book and is an independent and self-sufficient description of the most efficient theoretical methods of the strong-field and multiphoton physics. This book can serve as a textbook for graduate students

  8. Analysis of the physical atomic forces between noble gas atoms, alkali ions and halogen ions

    Science.gov (United States)

    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.

  9. Atomic force microscopy and force spectroscopy on the assessment of protein folding and functionality.

    Science.gov (United States)

    Carvalho, Filomena A; Martins, Ivo C; Santos, Nuno C

    2013-03-01

    Atomic force microscopy (AFM) applied to biological systems can, besides generating high-quality and well-resolved images, be employed to study protein folding via AFM-based force spectroscopy. This approach allowed remarkable advances in the measurement of inter- and intramolecular interaction forces with piconewton resolution. The detection of specific interaction forces between molecules based on the AFM sensitivity and the manipulation of individual molecules greatly advanced the understanding of intra-protein and protein-ligand interactions. Apart from the academic interest in the resolution of basic scientific questions, this technique has also key importance on the clarification of several biological questions of immediate biomedical relevance. Force spectroscopy is an especially appropriate technique for "mechanical proteins" that can provide crucial information on single protein molecules and/or domains. Importantly, it also has the potential of combining in a single experiment spatial and kinetic measurements. Here, the main principles of this methodology are described, after which the ability to measure interactions at the single-molecule level is discussed, in the context of relevant protein-folding examples. We intend to demonstrate the potential of AFM-based force spectroscopy in the study of protein folding, especially since this technique is able to circumvent some of the difficulties typically encountered in classical thermal/chemical denaturation studies. Copyright © 2012 Elsevier Inc. All rights reserved.

  10. Investigation of graphite composite anodes surfaces by atomic force microscopy and related techniques

    Energy Technology Data Exchange (ETDEWEB)

    Hirasawa, Karen Akemi; Nishioka, Keiko; Sato, Tomohiro; Yamaguchi, Shoji; Mori, Shoichiro [Mitsubishi Chemical Corp., Tsukuba Research Center, Ibaraki (Japan)

    1997-11-01

    The surface of a synthetic graphite (KS-44) and polyvinylidene difluoride binder (PVDF) anode for lithium-ion secondary batteries is imaged using atomic force microscopy (AFM) and several related scanning probe microscope (SPM) instruments including: dynamic force microscopy (DFM), friction force microscopy (FFM), laterally-modulated friction force microscopy (LM-FFM), visco-elasticity atomic force microscopy (VE-AFM), and AFM/simultaneous current measurement mode (SCM). DFM is found to be an exceptional mode for topographic imaging while FFM results in the clearest contrast distinction between PVDF binder and KS-44 graphite regions. (orig.)

  11. Electrical characterization of grain boundaries of CZTS thin films using conductive atomic force microscopy techniques

    Energy Technology Data Exchange (ETDEWEB)

    Muhunthan, N.; Singh, Om Pal [Compound Semiconductor Solar Cell, Physics of Energy Harvesting Division, New Delhi 110012 (India); Toutam, Vijaykumar, E-mail: toutamvk@nplindia.org [Quantum Phenomena and Applications Division, CSIR-National Physical Laboratory, Dr. K.S. Krishnan Marg, New Delhi 110012 (India); Singh, V.N., E-mail: singhvn@nplindia.org [Compound Semiconductor Solar Cell, Physics of Energy Harvesting Division, New Delhi 110012 (India)

    2015-10-15

    Graphical abstract: Experimental setup for conducting AFM (C-AFM). - Highlights: • Cu{sub 2}ZnSnS{sub 4} (CZTS) thin film was grown by reactive co-sputtering. • The electronic properties were probed using conducting atomic force microscope, scanning Kelvin probe microscopy and scanning capacitance microscopy. • C-AFM current flow mainly through grain boundaries rather than grain interiors. • SKPM indicated higher potential along the GBs compared to grain interiors. • The SCM explains that charge separation takes place at the interface of grain and grain boundary. - Abstract: Electrical characterization of grain boundaries (GB) of Cu-deficient CZTS (Copper Zinc Tin Sulfide) thin films was done using atomic force microscopic (AFM) techniques like Conductive atomic force microscopy (CAFM), Kelvin probe force microscopy (KPFM) and scanning capacitance microscopy (SCM). Absorbance spectroscopy was done for optical band gap calculations and Raman, XRD and EDS for structural and compositional characterization. Hall measurements were done for estimation of carrier mobility. CAFM and KPFM measurements showed that the currents flow mainly through grain boundaries (GB) rather than grain interiors. SCM results showed that charge separation mainly occurs at the interface of grain and grain boundaries and not all along the grain boundaries.

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

    Science.gov (United States)

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

    2013-10-08

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

  13. Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

    Science.gov (United States)

    Lemkul, Justin A; MacKerell, Alexander D

    2017-05-09

    Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus yielding the forces governing its dynamics, using classical physics rather than more expensive quantum mechanical calculations that are computationally intractable for large systems. Most force fields used to simulate biomolecular systems use fixed atomic partial charges, neglecting the influence of electronic polarization, instead making use of a mean-field approximation that may not be transferable across environments. Recent hardware and software developments make polarizable simulations feasible, and to this end, polarizable force fields represent the next generation of molecular dynamics simulation technology. In this work, we describe the refinement of a polarizable force field for DNA based on the classical Drude oscillator model by targeting quantum mechanical interaction energies and conformational energy profiles of model compounds necessary to build a complete DNA force field. The parametrization strategy employed in the present work seeks to correct weak base stacking in A- and B-DNA and the unwinding of Z-DNA observed in the previous version of the force field, called Drude-2013. Refinement of base nonbonded terms and reparametrization of dihedral terms in the glycosidic linkage, deoxyribofuranose rings, and important backbone torsions resulted in improved agreement with quantum mechanical potential energy surfaces. Notably, we expand on previous efforts by explicitly including Z-DNA conformational energetics in the refinement.

  14. Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

    Science.gov (United States)

    Wallace, Jason A; Shen, Jana K

    2012-11-14

    Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pK(a) values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future.

  15. The development of the spatially correlated adjustment wavelet filter for atomic force microscopy data

    Energy Technology Data Exchange (ETDEWEB)

    Sikora, Andrzej, E-mail: sikora@iel.wroc.pl [Electrotechnical Institute, Division of Electrotechnology and Materials Science, M. Skłodowskiej-Curie 55/61, 50-369 Wrocław (Poland); Rodak, Aleksander [Faculty of Electronics, Wrocław University of Technology, Janiszewskiego 11/17, 50-372 Wrocław (Poland); Unold, Olgierd [Institute of Computer Engineering, Control and Robotics, Faculty of Electronics, Wrocław University of Technology, Janiszewskiego 11/17, 50-372 Wrocław (Poland); Klapetek, Petr [Czech Metrology Institute, Okružní 31, 638 00 Brno (Czech Republic)

    2016-12-15

    In this paper a novel approach for the practical utilization of the 2D wavelet filter in terms of the artifacts removal from atomic force microscopy measurements results is presented. The utilization of additional data such as summary photodiode signal map is implemented in terms of the identification of the areas requiring the data processing, filtering settings optimization and the verification of the process performance. Such an approach allows to perform the filtering parameters adjustment by average user, while the straightforward method requires an expertise in this field. The procedure was developed as the function of the Gwyddion software. The examples of filtering the phase imaging and Electrostatic Force Microscopy measurement result are presented. As the wavelet filtering feature may remove a local artifacts, its superior efficiency over similar approach with 2D Fast Fourier Transformate based filter (2D FFT) can be noticed. - Highlights: • A novel approach to 2D wavelet-based filter for atomic force microscopy is shown. • The additional AFM measurement signal is used to adjust the filter. • Efficient removal of the local interference phenomena caused artifacts is presented.

  16. The development of the spatially correlated adjustment wavelet filter for atomic force microscopy data

    International Nuclear Information System (INIS)

    Sikora, Andrzej; Rodak, Aleksander; Unold, Olgierd; Klapetek, Petr

    2016-01-01

    In this paper a novel approach for the practical utilization of the 2D wavelet filter in terms of the artifacts removal from atomic force microscopy measurements results is presented. The utilization of additional data such as summary photodiode signal map is implemented in terms of the identification of the areas requiring the data processing, filtering settings optimization and the verification of the process performance. Such an approach allows to perform the filtering parameters adjustment by average user, while the straightforward method requires an expertise in this field. The procedure was developed as the function of the Gwyddion software. The examples of filtering the phase imaging and Electrostatic Force Microscopy measurement result are presented. As the wavelet filtering feature may remove a local artifacts, its superior efficiency over similar approach with 2D Fast Fourier Transformate based filter (2D FFT) can be noticed. - Highlights: • A novel approach to 2D wavelet-based filter for atomic force microscopy is shown. • The additional AFM measurement signal is used to adjust the filter. • Efficient removal of the local interference phenomena caused artifacts is presented.

  17. Visualising the Micro World of Chemical/Geochemical Interactions Using Atomic Force Microscopy (AFM)

    Energy Technology Data Exchange (ETDEWEB)

    Graham, G M; Sorbie, K S

    1997-12-31

    Scanning force microscopy, in particular AFM (Atomic Force Microscopy), provides a particular useful and interesting tool for the examination of surface structure at the near-atomic level. AFM is particularly well suited to the study of interactions at the surface in aqueous solutions using real time in-situ measurements. In this paper there is presented AFM images showing in situ crystal growth from supersaturated BaSO{sub 4} solutions onto the surface of barite. Growth structures in the form of spiral crystal growth features, presumably originating from screw dislocations, are illustrated. AFM images of novel scale crystal growth inhibition experiments are presented. Examination of the manner in which generically different species adsorb onto growth structures may help to explain mechanistic differences in the way which different inhibitor species perform against barium sulphate scale formation. Adsorption of polyacrylamide species onto mica surfaces have been viewed. The general utility of AFM to a number of other common surface interactions in oil field chemistry will be discussed. 17 refs., 3 figs.

  18. Long Range Forces between Atomic Impurities in Liquid Helium

    International Nuclear Information System (INIS)

    Dupont-Roc, J.

    2002-01-01

    Van der Waals or Casimir interaction between neutral quantum objects in their ground state is known to be universally attractive. This is not necessarily so when these objects are embedded in a polarizable medium. We show that atomic impurities in liquid helium may indeed realize repulsive forces, and even Van der Waals and Casimir forces with different signs. (author)

  19. Harmonic and power balance tools for tapping-mode atomic force microscope

    International Nuclear Information System (INIS)

    Sebastian, A.; Salapaka, M. V.; Chen, D. J.; Cleveland, J. P.

    2001-01-01

    The atomic force microscope (AFM) is a powerful tool for investigating surfaces at atomic scales. Harmonic balance and power balance techniques are introduced to analyze the tapping-mode dynamics of the atomic force microscope. The harmonic balance perspective explains observations hitherto unexplained in the AFM literature. A nonconservative model for the cantilever - sample interaction is developed. The energy dissipation in the sample is studied and the resulting power balance equations combined with the harmonic balance equations are used to estimate the model parameters. Experimental results confirm that the harmonic and power balance tools can be used effectively to predict the behavior of the tapping cantilever. [copyright] 2001 American Institute of Physics

  20. Stitching Grid-wise Atomic Force Microscope Images

    DEFF Research Database (Denmark)

    Vestergaard, Mathias Zacho; Bengtson, Stefan Hein; Pedersen, Malte

    2016-01-01

    Atomic Force Microscopes (AFM) are able to capture images with a resolution in the nano metre scale. Due to this high resolution, the covered area per image is relatively small, which can be problematic when surveying a sample. A system able to stitch AFM images has been developed to solve this p...

  1. Building machine learning force fields for nanoclusters

    Science.gov (United States)

    Zeni, Claudio; Rossi, Kevin; Glielmo, Aldo; Fekete, Ádám; Gaston, Nicola; Baletto, Francesca; De Vita, Alessandro

    2018-06-01

    We assess Gaussian process (GP) regression as a technique to model interatomic forces in metal nanoclusters by analyzing the performance of 2-body, 3-body, and many-body kernel functions on a set of 19-atom Ni cluster structures. We find that 2-body GP kernels fail to provide faithful force estimates, despite succeeding in bulk Ni systems. However, both 3- and many-body kernels predict forces within an ˜0.1 eV/Å average error even for small training datasets and achieve high accuracy even on out-of-sample, high temperature structures. While training and testing on the same structure always provide satisfactory accuracy, cross-testing on dissimilar structures leads to higher prediction errors, posing an extrapolation problem. This can be cured using heterogeneous training on databases that contain more than one structure, which results in a good trade-off between versatility and overall accuracy. Starting from a 3-body kernel trained this way, we build an efficient non-parametric 3-body force field that allows accurate prediction of structural properties at finite temperatures, following a newly developed scheme [A. Glielmo et al., Phys. Rev. B 95, 214302 (2017)]. We use this to assess the thermal stability of Ni19 nanoclusters at a fractional cost of full ab initio calculations.

  2. Observation and Manipulation of Polymers by Scanning Tunneling and Atomic Force Microscopy

    Science.gov (United States)

    1988-07-13

    Observation and Manipulation of Polymers by Scanning Tunneling and Atomic Force Microscooy 12. PERSONAL AUTHOR(S) M.M. Dovek, T.R. Albrecht, S.W.J. Kuan, C.A...COUNT FIELD GOP SU8 -GROUP 19. ABSTRACT (Continue on reverse if ncosay and kIti1I by block numbor) ~AM\\~ v~~\\~A Dhe properties of monolayer films of...organic materi s are importantl i--V~ ety of technologies. We have employed the STM and AFM t study’ LanD~ ..-odgett films of a varie ’ty of polymers

  3. All-atom normal-mode analysis reveals an RNA-induced allostery in a bacteriophage coat protein.

    Science.gov (United States)

    Dykeman, Eric C; Twarock, Reidun

    2010-03-01

    Assembly of the T=3 bacteriophage MS2 is initiated by the binding of a 19 nucleotide RNA stem loop from within the phage genome to a symmetric coat protein dimer. This binding event effects a folding of the FG loop in one of the protein subunits of the dimer and results in the formation of an asymmetric dimer. Since both the symmetric and asymmetric forms of the dimer are needed for the assembly of the protein container, this allosteric switch plays an important role in the life cycle of the phage. We provide here details of an all-atom normal-mode analysis of this allosteric effect. The results suggest that asymmetric contacts between the A -duplex RNA phosphodiester backbone of the stem loop with the EF loop in one coat protein subunit results in an increased dynamic behavior of its FG loop. The four lowest-frequency modes, which encompass motions predominantly on the FG loops, account for over 90% of the increased dynamic behavior due to a localization of the vibrational pattern on a single FG loop. Finally, we show that an analysis of the allosteric effect using an elastic network model fails to predict this localization effect, highlighting the importance of using an all-atom full force field method for this problem.

  4. Compensator design for improved counterbalancing in high speed atomic force microscopy

    OpenAIRE

    Bozchalooi, I. S.; Youcef-Toumi, K.; Burns, D. J.; Fantner, G. E.

    2011-01-01

    High speed atomic force microscopy can provide the possibility of many new scientific observations and applications ranging from nano-manufacturing to the study of biological processes. However, the limited imaging speed has been an imperative drawback of the atomic force microscopes. One of the main reasons behind this limitation is the excitation of the AFM dynamics at high scan speeds, severely undermining the reliability of the acquired images. In this research, we propose a piezo based, ...

  5. Local detection of X-ray spectroscopies with an in-situ Atomic Force Microscope

    International Nuclear Information System (INIS)

    Rodrigues, M S; Dhez, O; Denmat, S Le; Felici, R; Comin, F; Chevrier, J

    2008-01-01

    The in situ combination of Scanning Probe Microscopies with X-ray microbeams adds a variety of new possibilities to the panoply of synchrotron radiation techniques. This paper describes an optics-free Atomic Force Microscope that can be directly installed on most of the synchrotron radiation end-stations for combined X-ray and atomic force microscopy experiments. The instrument can be used for atomic force imaging of the investigated sample or to locally measure the X-ray absorption or diffraction, or it can also be used to mechanically interact with the sample while simultaneously taking spectroscopy or diffraction measurements. The local character of these measurements is intrinsically linked with the use of the Atomic Force Microscope tip. It is the sharp tip that gives the opportunity to measure the photons flux impinging on it, or to locally measure the absorption coefficient or the shape of the diffraction pattern. At the end an estimation of the limits of the various techniques presented is also discussed.

  6. Contrast artifacts in tapping tip atomic force microscopy

    DEFF Research Database (Denmark)

    Kyhle, Anders; Sørensen, Alexis Hammer; Zandbergen, Julie Bjerring

    1998-01-01

    When recording images with an atomic force microscope using the resonant vibrating cantilever mode, surprising strange results are often achieved. Typical artifacts are strange contours, unexpected height shifts, and sudden changes of the apparent resolution in the acquired images. Such artifacts...

  7. Atomic Force Microscopy Based Nanorobotics Modelling, Simulation, Setup Building and Experiments

    CERN Document Server

    Xie, Hui; Régnier, Stéphane; Sitti, Metin

    2012-01-01

    The atomic force microscope (AFM) has been successfully used to perform nanorobotic manipulation operations on nanoscale entities such as particles, nanotubes, nanowires, nanocrystals, and DNA since 1990s. There have been many progress on modeling, imaging, teleoperated or automated control, human-machine interfacing, instrumentation, and applications of AFM based nanorobotic manipulation systems in literature. This book aims to include all of such state-of-the-art progress in an organized, structured, and detailed manner as a reference book and also potentially a textbook in nanorobotics and any other nanoscale dynamics, systems and controls related research and education. Clearly written and well-organized, this text introduces designs and prototypes of the nanorobotic systems in detail with innovative principles of three-dimensional manipulation force microscopy and parallel imaging/manipulation force microscopy.

  8. Conservative and dissipative force field for simulation of coarse-grained alkane molecules: A bottom-up approach

    Energy Technology Data Exchange (ETDEWEB)

    Trément, Sébastien; Rousseau, Bernard, E-mail: bernard.rousseau@u-psud.fr [Laboratoire de Chimie-Physique, UMR 8000 CNRS, Université Paris-Sud, Orsay (France); Schnell, Benoît; Petitjean, Laurent; Couty, Marc [Manufacture Française des Pneumatiques MICHELIN, Centre de Ladoux, 23 place des Carmes, 63000 Clermont-Ferrand (France)

    2014-04-07

    We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems.

  9. Lorentz force actuation of a heated atomic force microscope cantilever.

    Science.gov (United States)

    Lee, Byeonghee; Prater, Craig B; King, William P

    2012-02-10

    We report Lorentz force-induced actuation of a silicon microcantilever having an integrated resistive heater. Oscillating current through the cantilever interacts with the magnetic field around a NdFeB permanent magnet and induces a Lorentz force that deflects the cantilever. The same current induces cantilever heating. With AC currents as low as 0.2 mA, the cantilever can be oscillated as much as 80 nm at resonance with a DC temperature rise of less than 5 °C. By comparison, the AC temperature variation leads to a thermomechanical oscillation that is about 1000 times smaller than the Lorentz deflection at the cantilever resonance. The cantilever position in the nonuniform magnetic field affects the Lorentz force-induced deflection, with the magnetic field parallel to the cantilever having the largest effect on cantilever actuation. We demonstrate how the cantilever actuation can be used for imaging, and for measuring the local material softening temperature by sensing the contact resonance shift.

  10. An overview of molecular dynamics simulations of oxidized lipid systems, with a comparison of ELBA and MARTINI force fields for coarse grained lipid simulations

    DEFF Research Database (Denmark)

    Siani, Pablo; de Souza, R M; Dias, L G

    2016-01-01

    our new data of all-atom and coarse-grained simulations of hydroperoxidized lipid monolayer and bilayer systems and (iii) provide a comparison of the MARTINI and ELBA coarse grained force fields for lipid bilayer systems. We show that the better electrostatic treatment of interactions in ELBA is able...

  11. Atom Skimmers and Atom Lasers Utilizing Them

    Science.gov (United States)

    Hulet, Randall; Tollett, Jeff; Franke, Kurt; Moss, Steve; Sackett, Charles; Gerton, Jordan; Ghaffari, Bita; McAlexander, W.; Strecker, K.; Homan, D.

    2005-01-01

    Atom skimmers are devices that act as low-pass velocity filters for atoms in thermal atomic beams. An atom skimmer operating in conjunction with a suitable thermal atomic-beam source (e.g., an oven in which cesium is heated) can serve as a source of slow atoms for a magneto-optical trap or other apparatus in an atomic-physics experiment. Phenomena that are studied in such apparatuses include Bose-Einstein condensation of atomic gases, spectra of trapped atoms, and collisions of slowly moving atoms. An atom skimmer includes a curved, low-thermal-conduction tube that leads from the outlet of a thermal atomic-beam source to the inlet of a magneto-optical trap or other device in which the selected low-velocity atoms are to be used. Permanent rare-earth magnets are placed around the tube in a yoke of high-magnetic-permeability material to establish a quadrupole or octupole magnetic field leading from the source to the trap. The atoms are attracted to the locus of minimum magnetic-field intensity in the middle of the tube, and the gradient of the magnetic field provides centripetal force that guides the atoms around the curve along the axis of the tube. The threshold velocity for guiding is dictated by the gradient of the magnetic field and the radius of curvature of the tube. Atoms moving at lesser velocities are successfully guided; faster atoms strike the tube wall and are lost from the beam.

  12. Structural analysis of γ radiation-induced chromosomal aberrations observed by atomic force microscopy

    International Nuclear Information System (INIS)

    Qu Shuang; Chen Ying; Ge Shili; Liu Xiulin; Zhou Pingkun; Zhang Sa; Zhang Detian

    2003-01-01

    Objective: To find a new method for the measurement of radiation-induced damage, the structures of normal chromosomes and 60 Co γ-ray-induced chromosomal aberration were analyzed by atomic force microscopy. Methods: Normal and irradiated chromosomes of human peripheral blood lymphocytes were prepared, then three-dimensional structure and height of chromosomes were analyzed by atomic force microscopy. Results: Three-dimensional structures of normal chromosomes and dicentric aberration in irradiated chromosomes were observed clearly. The data of chromosome height were helpful to recognizing the dicentric aberrations. Conclusion: Atomic force microscopy providing three-dimension image and linear measurement is a new and valuable tool for structural analysis of radiation-induced chromosomal aberrations

  13. Atomic Force Microscope Image Contrast Mechanisms on Supported Lipid Bilayers

    OpenAIRE

    Schneider, James; Dufrêne, Yves F.; Barger Jr., William R.; Lee, Gil U.

    2000-01-01

    This work presents a methodology to measure and quantitatively interpret force curves on supported lipid bilayers in water. We then use this method to correlate topographic imaging contrast in atomic force microscopy (AFM) images of phase-separated Langmuir-Blodgett bilayers with imaging load. Force curves collected on pure monolayers of both distearoylphosphatidylethanolamine (DSPE) and monogalactosylethanolamine (MGDG) and dioleoylethanolamine (DOPE) deposited at similar surface pressures o...

  14. A Novel Atomic Force Microscope with Multi-Mode Scanner

    International Nuclear Information System (INIS)

    Qin, Chun; Zhang, Haijun; Xu, Rui; Han, Xu; Wang, Shuying

    2016-01-01

    A new type of atomic force microscope (AFM) with multi-mode scanner is proposed. The AFM system provides more than four scanning modes using a specially designed scanner with three tube piezoelectric ceramics and three stack piezoelectric ceramics. Sample scanning of small range with high resolution can be realized by using tube piezos, meanwhile, large range scanning can be achieved by stack piezos. Furthermore, the combination with tube piezos and stack piezos not only realizes high-resolution scanning of small samples with large- scale fluctuation structure, but also achieves small range area-selecting scanning. Corresponding experiments are carried out in terms of four different scanning modes showing that the AFM is of reliable stability, high resolution and can be widely applied in the fields of micro/nano-technology. (paper)

  15. Spring constant calibration of atomic force microscope cantilevers of arbitrary shape

    Energy Technology Data Exchange (ETDEWEB)

    Sader, John E. [Department of Mathematics and Statistics, University of Melbourne, Victoria 3010 (Australia); Kavli Nanoscience Institute and Department of Physics, California Institute of Technology, Pasadena, California 91125 (United States); Sanelli, Julian A.; Adamson, Brian D.; Bieske, Evan J. [School of Chemistry, University of Melbourne, Victoria 3010 (Australia); Monty, Jason P.; Marusic, Ivan [Department of Mechanical Engineering, University of Melbourne, Victoria 3010 (Australia); Wei Xingzhan; Mulvaney, Paul [School of Chemistry, University of Melbourne, Victoria 3010 (Australia); Bio21 Institute, University of Melbourne, Victoria 3010 (Australia); Crawford, Simon A. [School of Botany, University of Melbourne, Victoria 3010 (Australia); Friend, James R. [Melbourne Centre for Nanofabrication, Clayton, Victoria 3800 (Australia); MicroNanophysics Research Laboratory, RMIT University, Melbourne, Victoria 3001 (Australia)

    2012-10-15

    The spring constant of an atomic force microscope cantilever is often needed for quantitative measurements. The calibration method of Sader et al. [Rev. Sci. Instrum. 70, 3967 (1999)] for a rectangular cantilever requires measurement of the resonant frequency and quality factor in fluid (typically air), and knowledge of its plan view dimensions. This intrinsically uses the hydrodynamic function for a cantilever of rectangular plan view geometry. Here, we present hydrodynamic functions for a series of irregular and non-rectangular atomic force microscope cantilevers that are commonly used in practice. Cantilever geometries of arrow shape, small aspect ratio rectangular, quasi-rectangular, irregular rectangular, non-ideal trapezoidal cross sections, and V-shape are all studied. This enables the spring constants of all these cantilevers to be accurately and routinely determined through measurement of their resonant frequency and quality factor in fluid (such as air). An approximate formulation of the hydrodynamic function for microcantilevers of arbitrary geometry is also proposed. Implementation of the method and its performance in the presence of uncertainties and non-idealities is discussed, together with conversion factors for the static and dynamic spring constants of these cantilevers. These results are expected to be of particular value to the design and application of micro- and nanomechanical systems in general.

  16. Spring constant calibration of atomic force microscope cantilevers of arbitrary shape

    International Nuclear Information System (INIS)

    Sader, John E.; Sanelli, Julian A.; Adamson, Brian D.; Bieske, Evan J.; Monty, Jason P.; Marusic, Ivan; Wei Xingzhan; Mulvaney, Paul; Crawford, Simon A.; Friend, James R.

    2012-01-01

    The spring constant of an atomic force microscope cantilever is often needed for quantitative measurements. The calibration method of Sader et al. [Rev. Sci. Instrum. 70, 3967 (1999)] for a rectangular cantilever requires measurement of the resonant frequency and quality factor in fluid (typically air), and knowledge of its plan view dimensions. This intrinsically uses the hydrodynamic function for a cantilever of rectangular plan view geometry. Here, we present hydrodynamic functions for a series of irregular and non-rectangular atomic force microscope cantilevers that are commonly used in practice. Cantilever geometries of arrow shape, small aspect ratio rectangular, quasi-rectangular, irregular rectangular, non-ideal trapezoidal cross sections, and V-shape are all studied. This enables the spring constants of all these cantilevers to be accurately and routinely determined through measurement of their resonant frequency and quality factor in fluid (such as air). An approximate formulation of the hydrodynamic function for microcantilevers of arbitrary geometry is also proposed. Implementation of the method and its performance in the presence of uncertainties and non-idealities is discussed, together with conversion factors for the static and dynamic spring constants of these cantilevers. These results are expected to be of particular value to the design and application of micro- and nanomechanical systems in general.

  17. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics.

    Science.gov (United States)

    Chen, Wei; Shen, Jana K

    2014-10-15

    Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force-shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK(a) values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via cotitrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle mesh Ewald, considering the known artifacts due to charge-compensating background plasma. Copyright © 2014 Wiley Periodicals, Inc.

  18. Atomic force microscope characterization of a resonating nanocantilever

    DEFF Research Database (Denmark)

    Abadal, G.; Davis, Zachary James; Borrise, X.

    2003-01-01

    An atomic force microscope (AFM) is used as a nanometer-scale resolution tool for the characterization of the electromechanical behaviour of a resonant cantilever-based mass sensor. The cantilever is actuated electrostatically by applying DC and AC voltages from a driver electrode placed closely...

  19. The Martini Coarse-Grained Force Field

    NARCIS (Netherlands)

    Periole, X.; Marrink, S.J.; Monticelli, Luca; Salonen, Emppu

    2013-01-01

    The Martini force field is a coarse-grained force field suited for molecular dynamics simulations of biomolecular systems. The force field has been parameterized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical

  20. Role of tip chemical reactivity on atom manipulation process in dynamic force microscopy

    Czech Academy of Sciences Publication Activity Database

    Sugimoto, Y.; Yurtsever, A.; Abe, M.; Morita, S.; Ondráček, Martin; Pou, P.; Perez, R.; Jelínek, Pavel

    2013-01-01

    Roč. 7, č. 8 (2013), s. 7370-7376 ISSN 1936-0851 R&D Projects: GA ČR(CZ) GPP204/11/P578 Grant - others:GA AV ČR(CZ) M100101207 Institutional support: RVO:68378271 Keywords : noncontact atomic force microscopy * atomic manipulation * force spectroscopy * chemical interaction force * DFT simulations * nudged elastic band Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 12.033, year: 2013 http://pubs.acs.org/doi/abs/10.1021/nn403097p

  1. Dielectrophoretic positioning of single nanoparticles on atomic force microscope tips for tip-enhanced Raman spectroscopy.

    Science.gov (United States)

    Leiterer, Christian; Deckert-Gaudig, Tanja; Singh, Prabha; Wirth, Janina; Deckert, Volker; Fritzsche, Wolfgang

    2015-05-01

    Tip-enhanced Raman spectroscopy, a combination of Raman spectroscopy and scanning probe microscopy, is a powerful technique to detect the vibrational fingerprint of molecules at the nanometer scale. A metal nanoparticle at the apex of an atomic force microscope tip leads to a large enhancement of the electromagnetic field when illuminated with an appropriate wavelength, resulting in an increased Raman signal. A controlled positioning of individual nanoparticles at the tip would improve the reproducibility of the probes and is quite demanding due to usually serial and labor-intensive approaches. In contrast to commonly used submicron manipulation techniques, dielectrophoresis allows a parallel and scalable production, and provides a novel approach toward reproducible and at the same time affordable tip-enhanced Raman spectroscopy tips. We demonstrate the successful positioning of an individual plasmonic nanoparticle on a commercial atomic force microscope tip by dielectrophoresis followed by experimental proof of the Raman signal enhancing capabilities of such tips. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Noncontact Atomic Force Microscopy: An Emerging Tool for Fundamental Catalysis Research.

    Science.gov (United States)

    Altman, Eric I; Baykara, Mehmet Z; Schwarz, Udo D

    2015-09-15

    Although atomic force microscopy (AFM) was rapidly adopted as a routine surface imaging apparatus after its introduction in 1986, it has not been widely used in catalysis research. The reason is that common AFM operating modes do not provide the atomic resolution required to follow catalytic processes; rather the more complex noncontact (NC) mode is needed. Thus, scanning tunneling microscopy has been the principal tool for atomic scale catalysis research. In this Account, recent developments in NC-AFM will be presented that offer significant advantages for gaining a complete atomic level view of catalysis. The main advantage of NC-AFM is that the image contrast is due to the very short-range chemical forces that are of interest in catalysis. This motivated our development of 3D-AFM, a method that yields quantitative atomic resolution images of the potential energy surfaces that govern how molecules approach, stick, diffuse, and rebound from surfaces. A variation of 3D-AFM allows the determination of forces required to push atoms and molecules on surfaces, from which diffusion barriers and variations in adsorption strength may be obtained. Pushing molecules towards each other provides access to intermolecular interaction between reaction partners. Following reaction, NC-AFM with CO-terminated tips yields textbook images of intramolecular structure that can be used to identify reaction intermediates and products. Because NC-AFM and STM contrast mechanisms are distinct, combining the two methods can produce unique insight. It is demonstrated for surface-oxidized Cu(100) that simultaneous 3D-AFM/STM yields resolution of both the Cu and O atoms. Moreover, atomic defects in the Cu sublattice lead to variations in the reactivity of the neighboring O atoms. It is shown that NC-AFM also allows a straightforward imaging of work function variations which has been used to identify defect charge states on catalytic surfaces and to map charge transfer within an individual

  3. Acoustic Imaging Frequency Dynamics of Ferroelectric Domains by Atomic Force Microscopy

    International Nuclear Information System (INIS)

    Kun-Yu, Zhao; Hua-Rong, Zeng; Hong-Zhang, Song; Sen-Xing, Hui; Guo-Rong, Li; Qing-Rui, Yin; Shimamura, Kiyoshi; Kannan, Chinna Venkadasamy; Villora, Encarnacion Antonia Garcia; Takekawa, Shunji; Kitamura, Kenji

    2008-01-01

    We report the acoustic imaging frequency dynamics of ferroelectric domains by low-frequency acoustic probe microscopy based on the commercial atomic force microscopy It is found that ferroelectric domain could be firstly visualized at lower frequency down to 0.5 kHz by AFM-based acoustic microscopy The frequency-dependent acoustic signal revealed a strong acoustic response in the frequency range from 7kHz to 10kHz, and reached maximum at 8.1kHz. The acoustic contrast mechanism can be ascribed to the different elastic response of ferroelectric microstructures to local elastic stress fields, which is induced by the acoustic wave transmitting in the sample when the piezoelectric transducer is vibrating and exciting acoustic wave under ac electric fields due to normal piezoelectric effects. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  4. Chromosome structure investigated with the atomic force microscope

    NARCIS (Netherlands)

    de Grooth, B.G.; Putman, C.A.J.; Putman, Constant A.; van der Werf, Kees; van Hulst, N.F.; van Oort, G.; van Oort, Geeske; Greve, Jan; Manne, Srinivas

    1992-01-01

    We have developed an atomic force microscope (AFM) with an integrated optical microscope. The optical microscope consists of an inverted epi-illumination system that yields images in reflection or fluorescence of the sample. With this system it is possible to quickly locate an object of interest. A

  5. An atomistic fingerprint algorithm for learning ab initio molecular force fields

    Science.gov (United States)

    Tang, Yu-Hang; Zhang, Dongkun; Karniadakis, George Em

    2018-01-01

    Molecular fingerprints, i.e., feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we present the density-encoded canonically aligned fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities. The fingerprint is essentially a continuous density field formed through the superimposition of smoothing kernels centered on the atoms. Rotational invariance of the fingerprint is achieved by aligning, for each fingerprint instance, the neighboring atoms onto a local canonical coordinate frame computed from a kernel minisum optimization procedure. We show that this approach is superior over principal components analysis-based methods especially when the atomistic neighborhood is sparse and/or contains symmetry. We propose that the "distance" between the density fields be measured using a volume integral of their pointwise difference. This can be efficiently computed using optimal quadrature rules, which only require discrete sampling at a small number of grid points. We also experiment on the choice of weight functions for constructing the density fields and characterize their performance for fitting interatomic potentials. The applicability of the fingerprint is demonstrated through a set of benchmark problems.

  6. Controlling stray electric fields on an atom chip for experiments on Rydberg atoms

    Science.gov (United States)

    Davtyan, D.; Machluf, S.; Soudijn, M. L.; Naber, J. B.; van Druten, N. J.; van Linden van den Heuvell, H. B.; Spreeuw, R. J. C.

    2018-02-01

    Experiments handling Rydberg atoms near surfaces must necessarily deal with the high sensitivity of Rydberg atoms to (stray) electric fields that typically emanate from adsorbates on the surface. We demonstrate a method to modify and reduce the stray electric field by changing the adsorbate distribution. We use one of the Rydberg excitation lasers to locally affect the adsorbed dipole distribution. By adjusting the averaged exposure time we change the strength (with the minimal value less than 0.2 V /cm at 78 μ m from the chip) and even the sign of the perpendicular field component. This technique is a useful tool for experiments handling Rydberg atoms near surfaces, including atom chips.

  7. Force and Compliance Measurements on Living Cells Using Atomic Force Microscopy (AFM

    Directory of Open Access Journals (Sweden)

    Wojcikiewicz Ewa P.

    2004-01-01

    Full Text Available We describe the use of atomic force microscopy (AFM in studies of cell adhesion and cell compliance. Our studies use the interaction between leukocyte function associated antigen-1 (LFA-1/intercellular adhesion molecule-1 (ICAM-1 as a model system. The forces required to unbind a single LFA-1/ICAM-1 bond were measured at different loading rates. This data was used to determine the dynamic strength of the LFA-1/ICAM-1 complex and characterize the activation potential that this complex overcomes during its breakage. Force measurements acquired at the multiple- bond level provided insight about the mechanism of cell adhesion. In addition, the AFM was used as a microindenter to determine the mechanical properties of cells. The applications of these methods are described using data from a previous study.

  8. Atomic force microscope featuring an integrated optical microscope

    NARCIS (Netherlands)

    Putman, C.A.J.; Putman, Constant A.J.; de Grooth, B.G.; van Hulst, N.F.; Greve, Jan

    1992-01-01

    The atomic force microscope (AFM) is used to image the surface of both conductors and nonconductors. Biological specimens constitute a large group of nonconductors. A disadvantage of most AFM's is the fact that relatively large areas of the sample surface have to be scanned to pinpoint a biological

  9. A transferable force field for CdS-CdSe-PbS-PbSe solid systems

    Science.gov (United States)

    Fan, Zhaochuan; Koster, Rik S.; Wang, Shuaiwei; Fang, Changming; Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W.; van Huis, Marijn A.; Vlugt, Thijs J. H.

    2014-12-01

    A transferable force field for the PbSe-CdSe solid system using the partially charged rigid ion model has been successfully developed and was used to study the cation exchange in PbSe-CdSe heteronanocrystals [A. O. Yalcin et al., "Atomic resolution monitoring of cation exchange in CdSe-PbSe heteronanocrystals during epitaxial solid-solid-vapor growth," Nano Lett. 14, 3661-3667 (2014)]. In this work, we extend this force field by including another two important binary semiconductors, PbS and CdS, and provide detailed information on the validation of this force field. The parameterization combines Bader charge analysis, empirical fitting, and ab initio energy surface fitting. When compared with experimental data and density functional theory calculations, it is shown that a wide range of physical properties of bulk PbS, PbSe, CdS, CdSe, and their mixed phases can be accurately reproduced using this force field. The choice of functional forms and parameterization strategy is demonstrated to be rational and effective. This transferable force field can be used in various studies on II-VI and IV-VI semiconductor materials consisting of CdS, CdSe, PbS, and PbSe. Here, we demonstrate the applicability of the force field model by molecular dynamics simulations whereby transformations are initiated by cation exchange.

  10. A transferable force field for CdS-CdSe-PbS-PbSe solid systems

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Zhaochuan; Vlugt, Thijs J. H., E-mail: t.j.h.vlugt@tudelft.nl [Process and Energy Department, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft,The Netherlands (Netherlands); Koster, Rik S.; Fang, Changming; Huis, Marijn A. van [Debye Institute for Nanomaterials Science and Center for Extreme Matter and Emergent Phenomena, Utrecht University, Princetonplein 5, 3584 CC Utrecht (Netherlands); Wang, Shuaiwei [Institute of Nanostructured Functional Materials, Huanghe Science and Technology College, Zhengzhou, Henan 450006 (China); Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W. [Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft (Netherlands)

    2014-12-28

    A transferable force field for the PbSe-CdSe solid system using the partially charged rigid ion model has been successfully developed and was used to study the cation exchange in PbSe-CdSe heteronanocrystals [A. O. Yalcin et al., “Atomic resolution monitoring of cation exchange in CdSe-PbSe heteronanocrystals during epitaxial solid-solid-vapor growth,” Nano Lett. 14, 3661–3667 (2014)]. In this work, we extend this force field by including another two important binary semiconductors, PbS and CdS, and provide detailed information on the validation of this force field. The parameterization combines Bader charge analysis, empirical fitting, and ab initio energy surface fitting. When compared with experimental data and density functional theory calculations, it is shown that a wide range of physical properties of bulk PbS, PbSe, CdS, CdSe, and their mixed phases can be accurately reproduced using this force field. The choice of functional forms and parameterization strategy is demonstrated to be rational and effective. This transferable force field can be used in various studies on II-VI and IV-VI semiconductor materials consisting of CdS, CdSe, PbS, and PbSe. Here, we demonstrate the applicability of the force field model by molecular dynamics simulations whereby transformations are initiated by cation exchange.

  11. Consistent force fields for saccharides

    DEFF Research Database (Denmark)

    Rasmussen, Kjeld

    1999-01-01

    Consistent force fields for carbohydrates were hitherto developed by extensive optimization ofpotential energy function parameters on experimental data and on ab initio results. A wide range of experimental data is used: internal structures obtained from gas phase electron diffraction and from x......-anomeric effects are accounted for without addition of specific terms. The work is done in the framework of the Consistent Force Field which originatedin Israel and was further developed in Denmark. The actual methods and strategies employed havebeen described previously. Extensive testing of the force field...

  12. Microstructural and micromechanical characterisation of TiAl alloys using atomic force microscopy and nanoindentation

    International Nuclear Information System (INIS)

    Gebhard, S.; Pyczak, F.; Goeken, M.

    2009-01-01

    Different microstructures were generated in the Ti-45Al-4.6Nb-0.2B-0.2C and Ti-45Al-1Cr alloys (at.%) by heat treatment. The microstructures were investigated using nanoindentation and atomic force microscopy which was compared with transmission electron microscopy. Topographic contrast is usually used for phase identification in the atomic force microscope. However, it was found that the topographic order of the phases changes with different microstructures and specimen preparations. Nanoindentation measurements provided local hardness values not obtainable by other methods and enabled clear distinction of the phases. The hardness values can give information on surrounding microstructure and solid solution hardening. The mean lamellar spacing of the colonies was measured using both atomic force microscopy and transmission electron microscopy. Atomic force microscopy was found to be suitable to determine the spacing between α 2 /γ-interfaces offering the advantages of easier sample preparation and fewer specimens compared to evaluation by TEM analysis.

  13. Nanodot deposition and its application with atomic force microscope

    Energy Technology Data Exchange (ETDEWEB)

    Liu Zenglei, E-mail: liuzenglei@sia.cn; Jiao Niandong, E-mail: ndjiao@sia.cn [Chinese Academy of Sciences, State Key Laboratory of Robotics, Shenyang Institute of Automation (China); Xu Ke [Shenyang Jianzhu University (China); Wang, Zhidong [Chiba Institute of Technology (Japan); Dong Zaili; Liu Lianqing [Chinese Academy of Sciences, State Key Laboratory of Robotics, Shenyang Institute of Automation (China)

    2013-06-15

    Nanodot deposition using atomic force microscope (AFM) is investigated. To realize repeatable and precise deposition of nanodots, the detailed control method is discussed. The electric field between AFM tip and substrate is analyzed, and a convenient method to control tip-substrate separation is proposed. In experiments, two nanodot matrixes are fabricated and the heights of the nanodots are analyzed. Experimental results testify that the control method can lead to repeatable and precise fabrication of deposited nanodots. As an application of deposited nanodots, a carbon nanotube (CNT) is soldered on gold electrodes with deposited Au nanodots. After soldering, the contact resistances between the CNT and the electrodes decrease greatly. AFM-based nanodot deposition can be used to fabricate special nanopatterns; also it can be used to solder nanomaterials on substrates to improve the electrical connection, which has a promising future for nanodevice fabrication.

  14. All-optical atom trap as a target for MOTRIMS-like collision experiments

    Science.gov (United States)

    Sharma, S.; Acharya, B. P.; De Silva, A. H. N. C.; Parris, N. W.; Ramsey, B. J.; Romans, K. L.; Dorn, A.; de Jesus, V. L. B.; Fischer, D.

    2018-04-01

    Momentum-resolved scattering experiments with laser-cooled atomic targets have been performed since almost two decades with magneto-optical trap recoil ion momentum spectroscopy (MOTRIMS) setups. Compared to experiments with gas-jet targets, MOTRIMS features significantly lower target temperatures allowing for an excellent recoil ion momentum resolution. However, the coincident and momentum-resolved detection of electrons was long rendered impossible due to incompatible magnetic field requirements. Here we report on an experimental approach which is based on an all-optical 6Li atom trap that—in contrast to magneto-optical traps—does not require magnetic field gradients in the trapping region. Atom temperatures of about 2 mK and number densities up to 109 cm-3 make this trap ideally suited for momentum-resolved electron-ion coincidence experiments. The overall configuration of the trap is very similar to conventional magneto-optical traps. It mainly requires small modifications of laser beam geometries and polarization which makes it easily implementable in other existing MOTRIMS experiments.

  15. Atomic force microscope-assisted scanning tunneling spectroscopy under ambient conditions.

    Science.gov (United States)

    Vakhshouri, Amin; Hashimoto, Katsushi; Hirayama, Yoshiro

    2014-12-01

    We have developed a method of atomic force microscopy (AFM)-assisted scanning tunneling spectroscopy (STS) under ambient conditions. An AFM function is used for rapid access to a selected position prior to performing STS. The AFM feedback is further used to suppress vertical thermal drift of the tip-sample distance during spectroscopy, enabling flexible and stable spectroscopy measurements at room temperature. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  16. Theoretical femtosecond physics atoms and molecules in strong laser fields

    CERN Document Server

    Grossmann, Frank

    2018-01-01

    This textbook extends from the basics of femtosecond physics all the way to some of the latest developments in the field. In this updated edition, the chapter on laser-driven atoms is augmented by the discussion of two-electron atoms interacting with strong and short laser pulses, as well as by a review of ATI rings and low energy structures in photo-electron spectra. In the chapter on laser-driven molecules a discussion of 2D infrared spectroscopy is incorporated. Theoretical investigations of atoms and molecules interacting with pulsed lasers up to atomic field strengths on the order of 10^16 W/cm² are leading to an understanding of many challenging experimental discoveries. The presentation starts with a brief introduction to pulsed laser physics. The basis for the non-perturbative treatment of laser-matter interaction in the book is the time-dependent Schrödinger equation. Its analytical as well as numerical solution are laid out in some detail. The light field is treated classically and different possi...

  17. Electromechanical Characterization of Single GaN Nanobelt Probed with Conductive Atomic Force Microscope

    Science.gov (United States)

    Yan, X. Y.; Peng, J. F.; Yan, S. A.; Zheng, X. J.

    2018-04-01

    The electromechanical characterization of the field effect transistor based on a single GaN nanobelt was performed under different loading forces by using a conductive atomic force microscope (C-AFM), and the effective Schottky barrier height (SBH) and ideality factor are simulated by the thermionic emission model. From 2-D current image, the high value of the current always appears on the nanobelt edge with the increase of the loading force less than 15 nN. The localized (I-V) characteristic reveals a typical rectifying property, and the current significantly increases with the loading force at the range of 10-190 nN. The ideality factor is simulated as 9.8 within the scope of GaN nano-Schottky diode unity (6.5-18), therefore the thermionic emission current is dominant in the electrical transport of the GaN-tip Schottky junction. The SBH is changed through the piezoelectric effect induced by the loading force, and it is attributed to the enhanced current. Furthermore, a single GaN nanobelt has a high mechanical-induced current ratio that could be made use of in a nanoelectromechanical switch.

  18. Cellulose fibril aggregation studies of eucalyptus dissolving pulps using atomic force microscopy

    CSIR Research Space (South Africa)

    Chunilall, Viren

    2006-11-01

    Full Text Available STUDIES OF Eucalyptus DISSOLVING PULPS USING ATOMIC FORCE MICROSCOPY V. Chunilall1, J.Wesley-Smith2, T. Bush1 1CSIR, Forestry and Forest Product Research Centre, P.O. Box 17001, Congella, 4013, South Africa. 2Electron Microscope Unit, University of Kwa... pulp using atomic force microscopy (AFM) have reported increased cellulose fibril aggregation during processing, and a concomitant decrease in surface area available for chemical reaction1,2. These findings were subsequently confirmed...

  19. Deriving force field parameters for coordination complexes

    DEFF Research Database (Denmark)

    Norrby, Per-Ola; Brandt, Peter

    2001-01-01

    The process of deriving molecular mechanics force fields for coordination complexes is outlined. Force field basics are introduced with an emphasis on special requirements for metal complexes. The review is then focused on how to set up the initial model, define the target, refine the parameters......, and validate the final force field, Alternatives to force field derivation are discussed briefly....

  20. Bimodal atomic force microscopy imaging of isolated antibodies in air and liquids

    International Nuclear Information System (INIS)

    MartInez, N F; Lozano, J R; Herruzo, E T; Garcia, F; Garcia, R; Richter, C; Sulzbach, T

    2008-01-01

    We have developed a dynamic atomic force microscopy (AFM) method based on the simultaneous excitation of the first two flexural modes of the cantilever. The instrument, called a bimodal atomic force microscope, allows us to resolve the structural components of antibodies in both monomer and pentameric forms. The instrument operates in both high and low quality factor environments, i.e., air and liquids. We show that under the same experimental conditions, bimodal AFM is more sensitive to compositional changes than amplitude modulation AFM. By using theoretical and numerical methods, we study the material contrast sensitivity as well as the forces applied on the sample during bimodal AFM operation

  1. Depletion interaction measured by colloidal probe atomic force microscopy

    NARCIS (Netherlands)

    Wijting, W.K.; Knoben, W.; Besseling, N.A.M.; Leermakers, F.A.M.; Cohen Stuart, M.A.

    2004-01-01

    We investigated the depletion interaction between stearylated silica surfaces in cyclohexane in the presence of dissolved polydimethylsiloxane by means of colloidal probe atomic force microscopy. We found that the range of the depletion interaction decreases with increasing concentration.

  2. Magnetic atom optics: mirrors, guides, traps, and chips for atoms

    Energy Technology Data Exchange (ETDEWEB)

    Hinds, E.A.; Hughes, I.G. [Sussex Centre for Optical and Atomic Physics, University of Sussex, Brighton (United Kingdom)

    1999-09-21

    For the last decade it has been possible to cool atoms to microkelvin temperatures ({approx}1 cm s{sup -1}) using a variety of optical techniques. Light beams provide the very strong frictional forces required to slow atoms from room temperature ({approx}500 m s{sup -1}). However, once the atoms are cold, the relatively weak conservative forces of static electric and magnetic fields play an important role. In our group we have been studying the interaction of cold rubidium atoms with periodically magnetized data storage media. Here we review the underlying principles of the forces acting on atoms above a suitably magnetized substrate or near current-carrying wires. We also summarize the status of experiments. These structures can be used as smooth or corrugated reflectors for controlling the trajectories of cold atoms. Alternatively, they may be used to confine atoms to a plane, a line, or a dot and in some cases to reach the quantum limit of confinement. Atoms levitated above a magnetized surface can be guided electrostatically by wires deposited on the surface. The flow and interaction of atoms in such a structure may form the basis of a new technology, 'integrated atom optics' which might ultimately be capable of realizing a quantum computer. (author)

  3. Formation of cold molecules through the photo-association of cold atoms of Cesium. Existence of long range forces between between cold excited atoms of Cesium; Formation de molecules froides par photoassociation d'atomes froids de cesium. Mise en evidence de forces a longue portee entre atomes froids excites de cesium

    Energy Technology Data Exchange (ETDEWEB)

    Comparat, D

    1999-09-01

    This thesis deals with the experimental study and the theoretical interpretation of the processes involved in photo-association and the formation of cold caesium molecules. It also presents a study of the dipolar forces between a pair of cold excited caesium atoms. We present here the first photo-association experiment on cold caesium atoms: two cold atoms absorb a photon to form an excited electronically excited molecules in a rotation-vibration level. The first production of cold molecules which was realised experimentally, after the spontaneous deexcitation of the photo-associated molecules, is described, stressing the role of the potential well of the molecular states O{sub g}{sup -}(6s+6p{sub 3/2}) or 1{sub u} (6s+6p{sub 3/2}) of caesium. The detection of the formed caesium molecules is based on a two-photons resonant ionisation that creates Cs{sub 2}{sup +} ions, afterwards selectively detected. Temperatures around 20-200 {mu}K have been measured. The photo-associative spectroscopy is described on the theoretical point of view: a detailed theoretical study allows to calculate precisely the asymptotic parts of the potential curves. On the experimental point of view, we present the spectroscopy of the extern potential well of the caesium state O{sub g}{sup -}(6s+6p{sub 3/2}) and the construction of an effective potential curve of the RKR type. A unified theory of photo-association in weak field, considered as a collision assisted by laser, is developed. The cold atoms experiments allow to study and control the collision between two atoms whose mutual interaction is of the dipole-dipole type. Two different physical systems are studied: a sample of Rydberg atoms, and the photo-association process which is a laser-assisted collision. A modification of the motion of one pair of atoms makes it possible to control the bipolar forces and to choose the atoms relative speeds. (author)

  4. Electrons and atoms in intense laser fields

    International Nuclear Information System (INIS)

    Davidovich, L.

    1982-11-01

    Several non-linear effects that show up when electrons and atoms interact with strong laser fields are considered. Thomson scattering, electron potential scattering in the presence of a laser beam, atomic ionization by strong laser fields, the refraction of electrons by laser beams and the Kapitza-Dirac effect are discussed. (Author) [pt

  5. Electrons and atoms in intense laser fields

    International Nuclear Information System (INIS)

    Davidovich, L.

    1982-01-01

    Several non-linear effects that show up when electrons and atoms interact with strong laser fields are considered. Thomson scattering, electron potential scattering in the presence of a laser beam, atomic ionization by strong laser fields, the refraction of electrons by laser beams and the Kapitza-Dirac effect are discussed. (Author) [pt

  6. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics †

    Science.gov (United States)

    Chen, Wei; Shen, Jana K.

    2014-01-01

    Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: 1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? 2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK a values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via co-titrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle-mesh Ewald, considering the known artifacts due to charge-compensating background plasma. PMID:25142416

  7. Cantilever contribution to the total electrostatic force measured with the atomic force microscope

    International Nuclear Information System (INIS)

    Guriyanova, Svetlana; Golovko, Dmytro S; Bonaccurso, Elmar

    2010-01-01

    The atomic force microscope (AFM) is a powerful tool for surface imaging at the nanometer scale and surface force measurements in the piconewton range. Among long-range surface forces, the electrostatic forces play a predominant role. They originate if the electric potentials of the substrate and of the tip of the AFM cantilever are different. A quantitative interpretation of the AFM signal is often difficult because it depends in a complicated fashion on the cantilever–tip–surface geometry. Since the electrostatic interaction is a long-range interaction, the cantilever, which is many microns from the surface, contributes to the total electrostatic force along with the tip. Here we present results of the electrostatic interaction between a conducting flat surface and horizontal or tilted cantilevers, with and without tips, at various distances from the surface. As addressed in a previous work, we show that the contribution of the cantilever to the overall force cannot be neglected. Based on a predictive model and on 3D confocal measurements, we discuss the influence of the tilting angle of the cantilever

  8. Polarization effects in molecular mechanical force fields

    Energy Technology Data Exchange (ETDEWEB)

    Cieplak, Piotr [Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92120 (United States); Dupradeau, Francois-Yves [UMR CNRS 6219-Faculte de Pharmacie, Universite de Picardie Jules Verne, 1 rue des Louvels, F-80037 Amiens (France); Duan, Yong [Genome Center and Department of Applied Science, University of California, Davis, One Shields Avenue, Davis, CA 95616 (United States); Wang Junmei, E-mail: pcieplak@burnham.or [Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Boulevard, ND9.136, Dallas, TX 75390-9050 (United States)

    2009-08-19

    The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component-polarization energy-and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations. (topical review)

  9. Vibrations of a molecule in an external force field.

    Science.gov (United States)

    Okabayashi, Norio; Peronio, Angelo; Paulsson, Magnus; Arai, Toyoko; Giessibl, Franz J

    2018-05-01

    The oscillation frequencies of a molecule on a surface are determined by the mass distribution in the molecule and the restoring forces that occur when the molecule bends. The restoring force originates from the atomic-scale interaction within the molecule and with the surface, which plays an essential role in the dynamics and reactivity of the molecule. In 1998, a combination of scanning tunneling microscopy with inelastic tunneling spectroscopy revealed the vibrational frequencies of single molecules adsorbed on a surface. However, the probe tip itself exerts forces on the molecule, changing its oscillation frequencies. Here, we combine atomic force microscopy with inelastic tunneling spectroscopy and measure the influence of the forces exerted by the tip on the lateral vibrational modes of a carbon monoxide molecule on a copper surface. Comparing the experimental data to a mechanical model of the vibrating molecule shows that the bonds within the molecule and with the surface are weakened by the proximity of the tip. This combination of techniques can be applied to analyze complex molecular vibrations and the mechanics of forming and loosening chemical bonds, as well as to study the mechanics of bond breaking in chemical reactions and atomic manipulation.

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

    Science.gov (United States)

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

    2010-07-28

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

  11. VEDA: a web-based virtual environment for dynamic atomic force microscopy.

    Science.gov (United States)

    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.

  12. Novel concepts in near-field optics: from magnetic near-field to optical forces

    Science.gov (United States)

    Yang, Honghua

    near-field response of a linear rod antenna is studied with Babinet's principle. Babinet's principle connects the magnetic field of a structure to the electric field of its complement structure. Using combined far- and near-field spectroscopy, imaging, and theory, I identify magnetic dipole and higher order bright and dark magnetic resonances at mid-infrared frequencies. From resonant length scaling and spatial field distributions, I confirm that the theoretical requirement of Babinet's principle for a structure to be infinitely thin and perfectly conducting is still fulfilled to a good approximation in the mid-infrared. Thus Babinet's principle provides access to spatial and spectral magnetic field properties, leading to targeted design and control of magnetic optical antennas. Lastly, a novel form of nanoscale optical spectroscopy based on mechanical detection of optical gradient force is explored. It is to measure the optical gradient force between induced dipole moments of a sample and an atomic force microscope (AFM) tip. My study provides the theoretical basis in terms of spectral behavior, resonant enhancement, and distance dependence of the optical gradient force from numerical simulations for a coupled nanoparticle model geometry. I show that the optical gradient force is dispersive for local electronic and vibrational resonances, yet can be absorptive for collective polaronic excitations. This spectral behavior together with the distance dependence scaling provides the key characteristics for its measurement and distinction from competing processes such as thermal expansion. Furthermore, I provide a perspective for resonant enhancement and control of optical forces in general.

  13. Formation of cold molecules through the photo-association of cold atoms of Cesium. Existence of long range forces between between cold excited atoms of Cesium

    International Nuclear Information System (INIS)

    Comparat, D.

    1999-09-01

    This thesis deals with the experimental study and the theoretical interpretation of the processes involved in photo-association and the formation of cold caesium molecules. It also presents a study of the dipolar forces between a pair of cold excited caesium atoms. We present here the first photo-association experiment on cold caesium atoms: two cold atoms absorb a photon to form an excited electronically excited molecules in a rotation-vibration level. The first production of cold molecules which was realised experimentally, after the spontaneous deexcitation of the photo-associated molecules, is described, stressing the role of the potential well of the molecular states O g - (6s+6p 3/2 ) or 1 u (6s+6p 3/2 ) of caesium. The detection of the formed caesium molecules is based on a two-photons resonant ionisation that creates Cs 2 + ions, afterwards selectively detected. Temperatures around 20-200 μK have been measured. The photo-associative spectroscopy is described on the theoretical point of view: a detailed theoretical study allows to calculate precisely the asymptotic parts of the potential curves. On the experimental point of view, we present the spectroscopy of the extern potential well of the caesium state O g - (6s+6p 3/2 ) and the construction of an effective potential curve of the RKR type. A unified theory of photo-association in weak field, considered as a collision assisted by laser, is developed. The cold atoms experiments allow to study and control the collision between two atoms whose mutual interaction is of the dipole-dipole type. Two different physical systems are studied: a sample of Rydberg atoms, and the photo-association process which is a laser-assisted collision. A modification of the motion of one pair of atoms makes it possible to control the bipolar forces and to choose the atoms relative speeds. (author)

  14. Atom ionization in a nonclassical intense electromagnetic field

    International Nuclear Information System (INIS)

    Popov, A.M.; Tikhonova, O.V.

    2002-01-01

    The atoms ionization process in the intense nonclassical electromagnetic field is considered. It is shown that depending on the field quantum state the probability of ionization may essentially change even by one and the same average quantum number in the radiation mode, whereby the difference in the ionization rates is especially significant in the case, when the ionization process is of a multiphoton character. It is demonstrates in particular, that the nonclassical field may be considerably more intensive from the viewpoint of the atoms ionization, than the classical field with the same intensity. The peculiarities of the decay, related to the atomic system state in the strong nonclassical field beyond the perturbation theory frames are studied [ru

  15. Scratch direction and threshold force in nanoscale scratching using atomic force microscopes

    Energy Technology Data Exchange (ETDEWEB)

    Tseng, Ampere A., E-mail: ampere.tseng@asu.edu [Department of Materials Science and Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan (China); Kuo, Chung-Feng Jeffrey; Jou, Shyankay [Department of Materials Science and Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan (China); Nishimura, Shinya; Shirakashi, Jun-ichi [Department of Electrical and Electronic Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588 (Japan)

    2011-09-01

    The nanoscaled tip in an AFM (atomic force microscope) has become an effective scratching tool for material removing in nanofabrication. In this article, the characteristics of using a diamond-coated pyramidal tip to scratch Ni-Fe thin film surfaces was experimentally investigated with the focus on the evaluation of the influence of the scratch or scan direction on the final shape of the scratched geometry as well as the applied scratch force. Results indicated that both the scratched profile and the scratch force were greatly affected by the scratch direction. It has been found that, to minimize the formation of protuberances along the groove sides and to have a better control of the scratched geometry, the tip face should be perpendicular to the scratching direction, which is also known as orthogonal cutting condition. To demonstrate the present findings, three groove patterns have been scratched with the tip face perpendicular to the scratching direction and very little amount of protuberances was observed. The threshold scratch force was also predicted based on the Hertz contact theory. Without considering the surface friction and adhesive forces between the tip and substrate, the threshold force predicted was twice smaller than the measurement value. Finally, recommendations for technical improvement and research focuses are provided.

  16. Scratch direction and threshold force in nanoscale scratching using atomic force microscopes

    International Nuclear Information System (INIS)

    Tseng, Ampere A.; Kuo, Chung-Feng Jeffrey; Jou, Shyankay; Nishimura, Shinya; Shirakashi, Jun-ichi

    2011-01-01

    The nanoscaled tip in an AFM (atomic force microscope) has become an effective scratching tool for material removing in nanofabrication. In this article, the characteristics of using a diamond-coated pyramidal tip to scratch Ni-Fe thin film surfaces was experimentally investigated with the focus on the evaluation of the influence of the scratch or scan direction on the final shape of the scratched geometry as well as the applied scratch force. Results indicated that both the scratched profile and the scratch force were greatly affected by the scratch direction. It has been found that, to minimize the formation of protuberances along the groove sides and to have a better control of the scratched geometry, the tip face should be perpendicular to the scratching direction, which is also known as orthogonal cutting condition. To demonstrate the present findings, three groove patterns have been scratched with the tip face perpendicular to the scratching direction and very little amount of protuberances was observed. The threshold scratch force was also predicted based on the Hertz contact theory. Without considering the surface friction and adhesive forces between the tip and substrate, the threshold force predicted was twice smaller than the measurement value. Finally, recommendations for technical improvement and research focuses are provided.

  17. Modelling atomic scale manipulation with the non-contact atomic force microscope

    International Nuclear Information System (INIS)

    Trevethan, T; Watkins, M; Kantorovich, L N; Shluger, A L; Polesel-Maris, J; Gauthier, S

    2006-01-01

    We present the results of calculations performed to model the process of lateral manipulation of an oxygen vacancy in the MgO(001) surface using the non-contact atomic force microscope (NC-AFM). The potential energy surfaces for the manipulation as a function of tip position are determined from atomistic modelling of the MgO(001) surface interacting with a Mg terminated MgO tip. These energies are then used to model the dynamical evolution of the system as the tip oscillates and at a finite temperature using a kinetic Monte Carlo method. The manipulation process is strongly dependent on the lateral position of the tip and the system temperature. It is also found that the expectation value of the point at which the vacancy jumps depends on the trajectory of the oscillating cantilever as the surface is approached. The effect of the manipulation on the operation of the NC-AFM is modelled with a virtual dynamic AFM, which explicitly simulates the entire experimental instrumentation and control loops. We show how measurable experimental signals can result from a single controlled atomic scale event and suggest the most favourable conditions for achieving successful atomic scale manipulation experimentally

  18. The all-too-flexible abductive method: ATOM's normative status.

    Science.gov (United States)

    Romeijn, Jan-Willem

    2008-09-01

    The author discusses the abductive theory of method (ATOM) by Brian Haig from a philosophical perspective, connecting his theory with a number of issues and trends in contemporary philosophy of science. It is argued that as it stands, the methodology presented by Haig is too permissive. Both the use of analogical reasoning and the application of exploratory factor analysis leave us with too many candidate theories to choose from, and explanatory coherence cannot be expected to save the day. The author ends with some suggestions to remedy the permissiveness and lack of normative force in ATOM, deriving from the experimental practice within which psychological data are produced.

  19. Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

    Directory of Open Access Journals (Sweden)

    Jörg Grunenberg

    2016-03-01

    Full Text Available We propose several new and promising antibacterial agents for the treatment of serious Gram-positive infections. Our predictions rely on force field simulations, supervised by first principle calculations and available experimental data. Different force fields were tested in order to reproduce linezolid's conformational space in terms of a the isolated and b the ribosomal bound state. In a first step, an all-atom model of the bacterial ribosome consisting of nearly 1600 atoms was constructed and evaluated. The conformational space of 30 different ribosomal/oxazolidinone complexes was scanned by stochastic methods, followed by an evaluation of their enthalpic penalties or rewards and the mechanical strengths of the relevant hydrogen bonds (relaxed force constants; compliance constants. The protocol was able to reproduce the experimentally known enantioselectivity favoring the S-enantiomer. In a second step, the experimentally known MIC values of eight linezolid analogues were used in order to crosscheck the robustness of our model. In a final step, this benchmarking led to the prediction of several new and promising lead compounds. Synthesis and biological evaluation of the new compounds are on the way.

  20. [Comparison of cell elasticity analysis methods based on atomic force microscopy indentation].

    Science.gov (United States)

    Wang, Zhe; Hao, Fengtao; Chen, Xiaohu; Yang, Zhouqi; Ding, Chong; Shang, Peng

    2014-10-01

    In order to investigate in greater detail the two methods based on Hertz model for analyzing force-distance curve obtained by atomic force microscopy, we acquired the force-distance curves of Hela and MCF-7 cells by atomic force microscopy (AFM) indentation in this study. After the determination of contact point, Young's modulus in different indentation depth were calculated with two analysis methods of "two point" and "slope fitting". The results showed that the Young's modulus of Hela cell was higher than that of MCF-7 cell,which is in accordance with the F-actin distribution of the two types of cell. We found that the Young's modulus of the cells was decreased with increasing indentation depth and the curve trends by "slope fitting". This indicated that the "slope fitting" method could reduce the error caused by the miscalculation of contact point. The purpose of this study was to provide a guidance for researcher to choose an appropriate method for analyzing AFM indentation force-distance curve.

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

    Science.gov (United States)

    2014-01-01

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

  2. Atomic force microscopy of torus-bearing pit membranes

    Science.gov (United States)

    Roland R. Dute; Thomas Elder

    2011-01-01

    Atomic force microscopy was used to compare the structures of dried, torus-bearing pit membranes from four woody species, three angiosperms and one gymnosperm. Tori of Osmanthus armatus are bipartite consisting of a pustular zone overlying parallel sets of microfibrils that form a peripheral corona. Microfibrils of the corona form radial spokes as they traverse the...

  3. Energy dissipation in multifrequency atomic force microscopy

    Directory of Open Access Journals (Sweden)

    Valentina Pukhova

    2014-04-01

    Full Text Available The instantaneous displacement, velocity and acceleration of a cantilever tip impacting onto a graphite surface are reconstructed. The total dissipated energy and the dissipated energy per cycle of each excited flexural mode during the tip interaction is retrieved. The tip dynamics evolution is studied by wavelet analysis techniques that have general relevance for multi-mode atomic force microscopy, in a regime where few cantilever oscillation cycles characterize the tip–sample interaction.

  4. Atomic mirrors for a Λ-type three-level atom

    International Nuclear Information System (INIS)

    Felemban, Nuha; Aldossary, Omar M; Lembessis, Vassilis E

    2014-01-01

    We propose atom mirror schemes for a three-level atom of Λ-type interacting with two evanescent fields, which are generated as a result of the total internal reflection of two coherent Gaussian laser beams at the interface of a dielectric prism with vacuum. The forces acting on the atom are derived by means of optical Bloch equations, based on the atomic density matrix elements. The theory is illustrated by setting up the equations of motion for 23 Na atom. Two types of excited schemes are examined, namely the cases in which the evanescent fields have polarization types of σ + −σ − and σ + −π. The equations are solved numerically and we get results for atomic trajectories for different parameters. The performance of the mirror for the two types of polarization schemes is quantified and discussed. The possibility of reflecting atoms at pre-determined directions is also discussed. (paper)

  5. Probing living bacterial adhesion by single cell force spectroscopy using atomic force microscopy

    DEFF Research Database (Denmark)

    Zeng, Guanghong; Ogaki, Ryosuke; Regina, Viduthalai R.

    be considered. We have therefore developed a simple and versatile method to make single-cell bacterial probes for measuring single cell adhesion with atomic force microscopy (AFM).[1] A single-cell probe was readily made by picking up a bacterial cell from a glass surface using a tipless AFM cantilever coated...... random immobilization is obtained by submerging the cantilever in a bacterial suspension. The reported method provides a general platform for investigating single cell interactions of bacteria with different surfaces and other cells by AFM force spectroscopy, thus improving our understanding....... The strain-dependent susceptibility to bacterial colonization on conventional PLL-g-PEG illustrates how bacterial diversity challenges development of “universal” antifouling coatings, and AFM single-cell force spectroscopy was proven to be a powerful tool to provide insights into the molecular mechanisms...

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

    Science.gov (United States)

    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.

  7. Dynamic polarizability of a complex atom in strong laser fields

    International Nuclear Information System (INIS)

    Rapoport, L.P.; Klinskikh, A.F.; Mordvinov, V.V.

    1997-01-01

    An asymptotic expansion of the dynamic polarizability of a complex atom in a strong circularly polarized light field is found for the case of high frequencies. The self-consistent approximation of the Hartree-Fock type for the ''atom+field'' system is developed, within the framework of which a numerical calculation of the dynamic polarizability of Ne, Kr, and Ar atoms in a strong radiation field is performed. The strong field effect is shown to manifest itself not only in a change of the energy spectrum and the character of behavior of the wave functions of atomic electrons, but also in a modification of the one-electron self-consistent potential for the atom in the field

  8. Note: Design of FPGA based system identification module with application to atomic force microscopy

    Science.gov (United States)

    Ghosal, Sayan; Pradhan, Sourav; Salapaka, Murti

    2018-05-01

    The science of system identification is widely utilized in modeling input-output relationships of diverse systems. In this article, we report field programmable gate array (FPGA) based implementation of a real-time system identification algorithm which employs forgetting factors and bias compensation techniques. The FPGA module is employed to estimate the mechanical properties of surfaces of materials at the nano-scale with an atomic force microscope (AFM). The FPGA module is user friendly which can be interfaced with commercially available AFMs. Extensive simulation and experimental results validate the design.

  9. Ehrenfest force in inhomogeneous magnetic field

    International Nuclear Information System (INIS)

    Sisakyan, A.N.; Shevchenko, O.Yu.; Samojlov, V.N.

    2000-01-01

    The Ehrenfest force in an inhomogeneous magnetic field is calculated. It is shown that there exist such (very rare) topologically nontrivial physical situations when the Gauss theorem in its classic formulation fails and, as a consequence, apart from the usual Lorentz force an additional, purely imaginary force acts on the charged particle. This force arises only in inhomogeneous magnetic fields of special configurations, has a purely quantum origin, and disappears in the classical limit

  10. Agreement between Ukraine and the International Atomic Energy Agency for the application of safeguards to all nuclear material in all peaceful nuclear activities of Ukraine

    International Nuclear Information System (INIS)

    1995-02-01

    The text of the Agreement between Ukraine and the International Atomic Energy Agency for the Application of Safeguards to all Nuclear Material in all Peaceful Nuclear Activities of Ukraine is reproduced in this document for the information of all Members. The Agreement was approved by the Agency's Board of Governors on 12 September 1994 and signed in Vienna on 28 September 1994. The Agreement entered into force, pursuant to Article 24, on 13 January 1995

  11. Energy dissipation unveils atomic displacement in the noncontact atomic force microscopy imaging of Si(111 )-(7 ×7 )

    Science.gov (United States)

    Arai, Toyoko; Inamura, Ryo; Kura, Daiki; Tomitori, Masahiko

    2018-03-01

    The kinetic energy of the oscillating cantilever of noncontact atomic force microscopy (nc-AFM) at room temperature was considerably dissipated over regions between a Si adatom and its neighboring rest atom for Si(111 )-(7 ×7 ) in close proximity to a Si tip on the cantilever. However, nc-AFM topographic images showed no atomic features over those regions, which were the hollow sites of the (7 ×7 ). This energy dissipation likely originated from displacement of Si adatoms with respect to the tip over the hollow sites, leading to a lateral shift of the adatoms toward the rest atom. This interaction led to hysteresis over each cantilever oscillation cycle; when the tip was retracted, the Si adatom likely returned to its original position. To confirm the atomic processes involved in the force interactions through Si dangling bonds, the Si(111 )-(7 ×7 ) surface was partly terminated with atomic hydrogen (H) and examined by nc-AFM. When the Si adatoms and/or the rest atoms were terminated with H, the hollow sites were not bright (less dissipation) in images of the energy dissipation channels by nc-AFM. The hollow sites acted as metastable sites for Si adatoms in surface diffusion and atom manipulation; thus, the dissipation energy which is saturated on the tip likely corresponds to the difference in the potential energy between the hollow site and the Si adatom site. In this study, we demonstrated the ability of dissipation channels of nc-AFM to enable visualization of the dynamics of atoms and molecules on surfaces, which cannot be revealed by nc-AFM topographic images alone.

  12. Atomic force microscopy on domains in biological model membranes

    NARCIS (Netherlands)

    Rinia, H.A.

    2001-01-01

    This thesis describes the preparation and imaging of supported lipid bilayers, which can be regarded as biological modelmembranes, in the light of the formation of domains. The bilayers were prepared with either the Langmuir-Blodgett method, or with vesicle fusion. They were imaged with Atomic Force

  13. An Atomic Force Microscopical Study of the Synaptonemal Complex

    NARCIS (Netherlands)

    Putman, C.A.J.; Putman, C.A.J.; Dietrich, A.J.J.; de Grooth, B.G.; van Marle, J.; Heyting, C.; van Hulst, N.F.; Greve, Jan

    1993-01-01

    The chromosomal structure which is specific for meiosis, the synaptonemal complex (SC), plays a major role in chromosome pairing and the recombination of genetic material. The SC was studied using atomic force microscopy (AFM). The results of this study confirm the results of light and electron

  14. Atomic Force Microscope for Imaging and Spectroscopy

    Science.gov (United States)

    Pike, W. T.; Hecht, M. H.; Anderson, M. S.; Akiyama, T.; Gautsch, S.; deRooij, N. F.; Staufer, U.; Niedermann, Ph.; Howald, L.; Mueller, D.

    2000-01-01

    We have developed, built, and tested an atomic force microscope (AFM) for extraterrestrial applications incorporating a micromachined tip array to allow for probe replacement. It is part of a microscopy station originally intended for NASA's 2001 Mars lander to identify the size, distribution, and shape of Martian dust and soil particles. As well as imaging topographically down to nanometer resolution, this instrument can be used to reveal chemical information and perform infrared and Raman spectroscopy at unprecedented resolution.

  15. Entanglement properties between two atoms in the binomial optical field interacting with two entangled atoms

    International Nuclear Information System (INIS)

    Liu Tang-Kun; Zhang Kang-Long; Tao Yu; Shan Chuan-Jia; Liu Ji-Bing

    2016-01-01

    The temporal evolution of the degree of entanglement between two atoms in a system of the binomial optical field interacting with two arbitrary entangled atoms is investigated. The influence of the strength of the dipole–dipole interaction between two atoms, probabilities of the Bernoulli trial, and particle number of the binomial optical field on the temporal evolution of the atomic entanglement are discussed. The result shows that the two atoms are always in the entanglement state. Moreover, if and only if the two atoms are initially in the maximally entangled state, the entanglement evolution is not affected by the parameters, and the degree of entanglement is always kept as 1. (paper)

  16. An atomic force microscope nanoscalpel for nanolithography and biological applications

    Energy Technology Data Exchange (ETDEWEB)

    Beard, J D; Burbridge, D J; Moskalenko, A V; Dudko, O; Gordeev, S N [Department of Physics, University of Bath, Bath BA2 7AY (United Kingdom); Yarova, P L; Smirnov, S V, E-mail: jdb28@bath.ac.u [Department of Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY (United Kingdom)

    2009-11-04

    We present the fabrication of specialized nanotools, termed nanoscalpels, and their application for nanolithography and nanomechanical manipulation of biological objects. Fabricated nanoscalpels have the shape of a thin blade with the controlled thickness of 20-30 nm and width of 100-200 nm. They were fabricated using electron beam induced deposition at the apex of atomic force microscope probes and are hard enough for a single cut to penetrate a {approx}45 nm thick gold layer; and thus can be used for making narrow electrode gaps required for fabrication of nanoelectronic devices. As an atomic force microscope-based technique the nanoscalpel provides simultaneous control of the applied cutting force and the depth of the cut. Using mammalian cells as an example, we demonstrated their ability to make narrow incisions and measurements of local elastic and inelastic characteristics of a cell, making nanoscalpels also useful as a nanosurgical tool in cell biology. Therefore, we believe that the nanoscalpel could serve as an important tool for nanofabrication and nanosurgery on biological objects.

  17. Surface structure investigations using noncontact atomic force microscopy

    International Nuclear Information System (INIS)

    Kolodziej, J.J.; Such, B.; Goryl, M.; Krok, F.; Piatkowski, P.; Szymonski, M.

    2006-01-01

    Surfaces of several A III B V compound semiconductors (InSb, GaAs, InP, InAs) of the (0 0 1) orientation have been studied with noncontact atomic force microscopy (NC-AFM). Obtained atomically resolved patterns have been compared with structural models available in the literature. It is shown that NC-AFM is an efficient tool for imaging complex surface structures in real space. It is also demonstrated that the recent structural models of III-V compound surfaces provide a sound base for interpretation of majority of features present in recorded patterns. However, there are also many new findings revealed by the NC-AFM method that is still new experimental technique in the context of surface structure determination

  18. Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding

    Directory of Open Access Journals (Sweden)

    Finkelstein Alexei V

    2007-07-01

    Full Text Available Abstract Background The prediction of ligand binding or protein structure requires very accurate force field potentials – even small errors in force field potentials can make a 'wrong' structure (from the billions possible more stable than the single, 'correct' one. However, despite huge efforts to optimize them, currently-used all-atom force fields are still not able, in a vast majority of cases, even to keep a protein molecule in its native conformation in the course of molecular dynamics simulations or to bring an approximate, homology-based model of protein structure closer to its native conformation. Results A strict analysis shows that a specific coupling of multi-atom Van der Waals interactions with covalent bonding can, in extreme cases, increase (or decrease the interaction energy by about 20–40% at certain angles between the direction of interaction and the covalent bond. It is also shown that on average multi-body effects decrease the total Van der Waals energy in proportion to the square root of the electronic component of dielectric permittivity corresponding to dipole-dipole interactions at small distances, where Van der Waals interactions take place. Conclusion The study shows that currently-ignored multi-atom Van der Waals interactions can, in certain instances, lead to significant energy effects, comparable to those caused by the replacement of atoms (for instance, C by N in conventional pairwise Van der Waals interactions.

  19. Classical and Quantum Chaos in Atom Optics

    OpenAIRE

    Saif, Farhan

    2006-01-01

    The interaction of an atom with an electromagnetic field is discussed in the presence of a time periodic external modulating force. It is explained that a control on atom by electromagnetic fields helps to design the quantum analog of classical optical systems. In these atom optical systems chaos may appear at the onset of external fields. The classical and quantum chaotic dynamics is discussed, in particular in an atom optics Fermi accelerator. It is found that the quantum dynamics exhibits ...

  20. Atomic forces between noble gas atoms, alkali ions, and halogen ions for surface interactions

    Science.gov (United States)

    Wilson, J. W.; Outlaw, R. A.; Heinbockel, J. H.

    1988-01-01

    The components of the physical forces between noble gas atoms, alkali ions, and halogen ions are analyzed and a data base developed from analysis of the two-body potential data, the alkali-halide molecular data, and the noble gas crystal and salt crystal data. A satisfactory global fit to this molecular and crystal data is then reproduced by the model to within several percent. Surface potentials are evaluated for noble gas atoms on noble gas surfaces and salt crystal surfaces with surface tension neglected. Within this context, the noble gas surface potentials on noble gas and salt crystals are considered to be accurate to within several percent.

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

    Science.gov (United States)

    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.

  2. How to cool down cold atoms using laser light? Principles and techniques

    International Nuclear Information System (INIS)

    Guellati-Khelifa, Saida; Clade, Pierre

    2012-01-01

    This article is devoted to the description of various mechanisms of the laser cooling of neutral atoms. These mechanisms are all based on the interaction between a photon, an entity of light, and an atom, an entity of matter. One of the macroscopic manifestations of this interaction is the pressure of radiation force. The effect of this force is strongly amplified when the source of photon is a laser. We will describe how it is possible to use this force with the Doppler effect in order to slow an atomic beam and also to reduce considerably the thermal agitation of atoms. We will explain how by shaping the light potentials and magnetic fields it is possible to reach extremely low temperatures of some nano-kelvin. At these temperatures, very near to the absolute zero, it is possible for certain kind of atoms, called bosons, to achieve a new state of matter, where quantum behaviour of atoms became apparent on a macroscopic scale. (authors)

  3. Optics with an Atom Laser Beam

    International Nuclear Information System (INIS)

    Bloch, Immanuel; Koehl, Michael; Greiner, Markus; Haensch, Theodor W.; Esslinger, Tilman

    2001-01-01

    We report on the atom optical manipulation of an atom laser beam. Reflection, focusing, and its storage in a resonator are demonstrated. Precise and versatile mechanical control over an atom laser beam propagating in an inhomogeneous magnetic field is achieved by optically inducing spin flips between atomic ground states with different magnetic moment. The magnetic force acting on the atoms can thereby be effectively switched on and off. The surface of the atom optical element is determined by the resonance condition for the spin flip in the inhomogeneous magnetic field. More than 98% of the incident atom laser beam is reflected specularly

  4. Toward Structure Prediction for Short Peptides Using the Improved SAAP Force Field Parameters

    Directory of Open Access Journals (Sweden)

    Kenichi Dedachi

    2013-01-01

    Full Text Available Based on the observation that Ramachandran-type potential energy surfaces of single amino acid units in water are in good agreement with statistical structures of the corresponding amino acid residues in proteins, we recently developed a new all-atom force field called SAAP, in which the total energy function for a polypeptide is expressed basically as a sum of single amino acid potentials and electrostatic and Lennard-Jones potentials between the amino acid units. In this study, the SAAP force field (SAAPFF parameters were improved, and classical canonical Monte Carlo (MC simulation was carried out for short peptide models, that is, Met-enkephalin and chignolin, at 300 K in an implicit water model. Diverse structures were reasonably obtained for Met-enkephalin, while three folded structures, one of which corresponds to a native-like structure with three native hydrogen bonds, were obtained for chignolin. The results suggested that the SAAP-MC method is useful for conformational sampling for the short peptides. A protocol of SAAP-MC simulation followed by structural clustering and examination of the obtained structures by ab initio calculation or simply by the number of the hydrogen bonds (or the hardness was demonstrated to be an effective strategy toward structure prediction for short peptide molecules.

  5. Atomic Force Microscopy for Soil Analysis

    Science.gov (United States)

    gazze, andrea; doerr, stefan; dudley, ed; hallin, ingrid; matthews, peter; quinn, gerry; van keulen, geertje; francis, lewis

    2016-04-01

    Atomic Force Microscopy (AFM) is a high-resolution surface-sensitive technique, which provides 3-dimensional topographical information and material properties of both stiff and soft samples in their natural environments. Traditionally AFM has been applied to samples with low roughness: hence its use for soil analysis has been very limited so far. Here we report the optimization settings required for a standardization of high-resolution and artefact-free analysis of natural soil with AFM: soil immobilization, AFM probe selection, artefact recognition and minimization. Beyond topography, AFM can be used in a spectroscopic mode to evaluate nanomechanical properties, such as soil viscosity, stiffness, and deformation. In this regards, Bruker PeakForce-Quantitative NanoMechanical (QNM) AFM provides a fast and convenient way to extract physical properties from AFM force curves in real-time to obtain soil nanomechanical properties. Here we show for the first time the ability of AFM to describe the topography of natural soil at nanometre resolution, with observation of micro-components, such as clays, and of nano-structures, possibly of biotic origin, the visualization of which would prove difficult with other instrumentations. Finally, nanomechanical profiling has been applied to different wettability states in soil and the respective physical patterns are discussed.

  6. Stimulated Raman spectroscopy and nanoscopy of molecules using near field photon induced forces without resonant electronic enhancement gain

    Energy Technology Data Exchange (ETDEWEB)

    Tamma, Venkata Ananth [CaSTL Center, Department of Chemistry, University of California, Irvine, California 92697 (United States); Huang, Fei; Kumar Wickramasinghe, H., E-mail: hkwick@uci.edu [Department of Electrical Engineering and Computer Science, 142 Engineering Tower, University of California, Irvine, California 92697 (United States); Nowak, Derek [Molecular Vista, Inc., 6840 Via Del Oro, San Jose, California 95119 (United States)

    2016-06-06

    We report on stimulated Raman spectroscopy and nanoscopy of molecules, excited without resonant electronic enhancement gain, and recorded using near field photon induced forces. Photon-induced interaction forces between the sharp metal coated silicon tip of an Atomic Force Microscope (AFM) and a sample resulting from stimulated Raman excitation were detected. We controlled the tip to sample spacing using the higher order flexural eigenmodes of the AFM cantilever, enabling the tip to come very close to the sample. As a result, the detection sensitivity was increased compared with previous work on Raman force microscopy. Raman vibrational spectra of azobenzene thiol and l-phenylalanine were measured and found to agree well with published results. Near-field force detection eliminates the need for far-field optical spectrometer detection. Recorded images show spatial resolution far below the optical diffraction limit. Further optimization and use of ultrafast pulsed lasers could push the detection sensitivity towards the single molecule limit.

  7. Agreement between Ukraine and the International Atomic Energy Agency for the application of safeguards to all nuclear material in all peaceful nuclear activities of Ukraine

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-02-01

    The text of the Agreement between Ukraine and the International Atomic Energy Agency for the Application of Safeguards to all Nuclear Material in all Peaceful Nuclear Activities of Ukraine is reproduced in this document for the information of all Members. The Agreement was approved by the Agency`s Board of Governors on 12 September 1994 and signed in Vienna on 28 September 1994. The Agreement entered into force, pursuant to Article 24, on 13 January 1995.

  8. Optical Measurements of Strong Radio-Frequency Fields Using Rydberg Atoms

    Science.gov (United States)

    Miller, Stephanie Anne

    There has recently been an initiative toward establishing atomic measurement standards for field quantities, including radio-frequency, millimeter-wave, and micro-wave electric fields. Current measurement standards are obtained using dipole antennas, which are fundamentally limited in frequency bandwidth (set by the physical size of the antenna) and accuracy (due to the metal perturbing the field during the measurement). Establishing an atomic standard rectifies these problems. My thesis work contributes to an ongoing effort towards establishing the viability of using Rydberg electromagnetically induced transparency (EIT) to perform atom-based measurements of radio-frequency (RF) fields over a wide range of frequencies and field strengths, focusing on strong-field measurements. Rydberg atoms are atoms with an electron excited to a high principal quantum number, resulting in a high sensitivity to an applied field. A model based on Floquet theory is implemented to accurately describe the observed atomic energy level shifts from which information about the field is extracted. Additionally, the effects due to the different electric field domains within the measurement volume are accurately modeled. Absolute atomic measurements of fields up to 296 V/m within a +/-0.35% relative uncertainty are demonstrated. This is the strongest field measured at the time of data publication. Moreover, the uncertainty is over an order of magnitude better than that of current standards. A vacuum chamber setup that I implemented during my graduate studies is presented and its unique components are detailed. In this chamber, cold-atom samples are generated and Rydberg atoms are optically excited within the ground-state sample. The Rydberg ion detection and imaging procedure are discussed, particularly the high magnification that the system provides. By analyzing the position of the ions, the spatial correlation g(2) (r) of Rydberg-atom distributions can be extracted. Aside from ion

  9. Atomic force microscopic investigation of commercial pressure sensitive adhesives for forensic analysis.

    Science.gov (United States)

    Canetta, Elisabetta; Adya, Ashok K

    2011-07-15

    Pressure sensitive adhesive (PSA), such as those used in packaging and adhesive tapes, are very often encountered in forensic investigations. In criminal activities, packaging tapes may be used for sealing packets containing drugs, explosive devices, or questioned documents, while adhesive and electrical tapes are used occasionally in kidnapping cases. In this work, the potential of using atomic force microscopy (AFM) in both imaging and force mapping (FM) modes to derive additional analytical information from PSAs is demonstrated. AFM has been used to illustrate differences in the ultrastructural and nanomechanical properties of three visually distinguishable commercial PSAs to first test the feasibility of using this technique. Subsequently, AFM was used to detect nanoscopic differences between three visually indistinguishable PSAs. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  10. Imaging three-dimensional surface objects with submolecular resolution by atomic force microscopy

    Czech Academy of Sciences Publication Activity Database

    Moreno, C.; Stetsovych, Oleksandr; Shimizu, T.K.; Custance, O.

    2015-01-01

    Roč. 15, č. 4 (2015), s. 2257-2262 ISSN 1530-6984 Institutional support: RVO:68378271 Keywords : noncontact atomic force microscopy (NC- AFM ) * submolecular resolution * three-dimensional dynamic force spectroscopy * high-resolution imaging Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 13.779, year: 2015

  11. Atomic force microscopy on chromosomes, chromatin and DNA: a review.

    Science.gov (United States)

    Kalle, Wouter; Strappe, Padraig

    2012-12-01

    The purpose of this review is to discuss the achievements and progress that has been made in the use of atomic force microscopy in DNA related research in the last 25 years. For this review DNA related research is split up in chromosomal-, chromatin- and DNA focused research to achieve a logical flow from large- to smaller structures. The focus of this review is not only on the AFM as imaging tool but also on the AFM as measuring tool using force spectroscopy, as therein lays its greatest advantage and future. The amazing technological and experimental progress that has been made during the last 25 years is too extensive to fully cover in this review but some key developments and experiments have been described to give an overview of the evolution of AFM use from 'imaging tool' to 'measurement tool' on chromosomes, chromatin and DNA. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

  12. Atomic hydrogen storage. [cryotrapping and magnetic field strength

    Science.gov (United States)

    Woollam, J. A. (Inventor)

    1980-01-01

    Atomic hydrogen, for use as a fuel or as an explosive, is stored in the presence of a strong magnetic field in exfoliated layered compounds such as molybdenum disulfide or an elemental layer material such as graphite. The compound is maintained at liquid temperatures and the atomic hydrogen is collected on the surfaces of the layered compound which are exposed during delamination (exfoliation). The strong magnetic field and the low temperature combine to prevent the atoms of hydrogen from recombining to form molecules.

  13. Interaction of strong electromagnetic fields with atoms

    International Nuclear Information System (INIS)

    Brandi, H.S.; Davidovich, L.; Zagury, N.

    1982-06-01

    Several non-linear processes involvoing the interaction of atoms with strong laser fields are discussed, with particular emphasis on the ionization problem. Non-perturbative methods which have been proposed to tackle this problem are analysed, and shown to correspond to an expansion in the intra-atomic potential. The relation between tunneling and multiphoton absorption as ionization mechanisms, and the generalization of Einstein's photoelectric equation to the strong-field case are discussed. (Author) [pt

  14. Examination of employment in the atomic energy field

    International Nuclear Information System (INIS)

    Baker, J.G.

    1978-02-01

    This study, which focuses on the years 1968--1975, singles out important employment trends in the atomic energy field and develops causal explanations for these trends. The study also provides a descriptive profile of employment in the field. Employment in the atomic energy field has grown from 138,519 in 1963 to 197,466 in 1975, an annual rate of 3.0 percent. The deployment of scientists, engineers, and technicians in the government-owned, contractor-operated (GOCO) sector changed little from 1968 to 1975. Private sector deployment altered considerably, with a large increase. Within the scientist group, the GOCO sector employment by field has changed little from 1968 to 1975. Private sector scientists have seen considerable alteration of their employment. There has been little change in the employment shares of engineering fields in the GOCO sector for the 1968 to 1975 period. Private sector engineers have seen much greater change, with civil engineers increasing their share 6% to 11%. Of all GOCO technicians, physical science technicians have increased their employment share from 12% to 17%. Of all private sector technicians, draftsmen have increased their share from 29% to 37% and reactor operators from 4% to 7%. Total employment in the field is shifting toward smaller firms. Employment by region has changed considerably in the private sector from 1968 to 1975. GOCO regional employment has also changed. The percentage of scientists and engineers involved in research and development has declined from 68% in 1968 to 39% in 1975. Three private sector industrial segments--reactor design and manufacturing, nuclear facilities design and engineering, and operation and maintenance of reactors--have experienced tremendous growth from 1968 to 1975. 8 figures, 32 tables

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

    OpenAIRE

    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 volta...

  16. Atomic force microscope image contrast mechanisms on supported lipid bilayers.

    Science.gov (United States)

    Schneider, J; Dufrêne, Y F; Barger, W R; Lee, G U

    2000-08-01

    This work presents a methodology to measure and quantitatively interpret force curves on supported lipid bilayers in water. We then use this method to correlate topographic imaging contrast in atomic force microscopy (AFM) images of phase-separated Langmuir-Blodgett bilayers with imaging load. Force curves collected on pure monolayers of both distearoylphosphatidylethanolamine (DSPE) and monogalactosylethanolamine (MGDG) and dioleoylethanolamine (DOPE) deposited at similar surface pressures onto a monolayer of DSPE show an abrupt breakthrough event at a repeatable, material-dependent force. The breakthrough force for DSPE and MGDG is sizable, whereas the breakthrough force for DOPE is too small to measure accurately. Contact-mode AFM images on 1:1 mixed monolayers of DSPE/DOPE and MGDG/DOPE have a high topographic contrast at loads between the breakthrough force of each phase, and a low topographic contrast at loads above the breakthrough force of both phases. Frictional contrast is inverted and magnified at loads above the breakthrough force of both phases. These results emphasize the important role that surface forces and mechanics can play in imaging multicomponent biomembranes with AFM.

  17. Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring

    DEFF Research Database (Denmark)

    Lanzarotti, Esteban; Marcatili, Paolo; Nielsen, Morten

    2018-01-01

    Interactions of T cell receptors (TCR) to peptides in complex with MHC (p:MHC) are key features that mediate cellular immune responses. While MHC binding is required for a peptide to be presented to T cells, not all MHC binders are immunogenic. The interaction of a TCR to the p:MHC complex holds...... terms. Building a benchmark of TCR:p:MHC complexes where epitopes and non-epitopes are modelled using state-of-the-art molecular modelling tools, scoring p:MHC to a given TCR using force-fields, optimized in a cross-validation setup to evaluate TCR inter atomic interactions involved with each p:MHC, we...... and model the TCR:p:MHC complex structure. In summary, we conclude that it is possible to identify the TCR cognate target among different candidate peptides by using a force-field based model, and believe this works could lay the foundation for future work within prediction of TCR:p:MHC interactions....

  18. Quantitative measurement of solvation shells using frequency modulated atomic force microscopy

    Science.gov (United States)

    Uchihashi, T.; Higgins, M.; Nakayama, Y.; Sader, J. E.; Jarvis, S. P.

    2005-03-01

    The nanoscale specificity of interaction measurements and additional imaging capability of the atomic force microscope make it an ideal technique for measuring solvation shells in a variety of liquids next to a range of materials. Unfortunately, the widespread use of atomic force microscopy for the measurement of solvation shells has been limited by uncertainties over the dimensions, composition and durability of the tip during the measurements, and problems associated with quantitative force calibration of the most sensitive dynamic measurement techniques. We address both these issues by the combined use of carbon nanotube high aspect ratio probes and quantifying the highly sensitive frequency modulation (FM) detection technique using a recently developed analytical method. Due to the excellent reproducibility of the measurement technique, additional information regarding solvation shell size as a function of proximity to the surface has been obtained for two very different liquids. Further, it has been possible to identify differences between chemical and geometrical effects in the chosen systems.

  19. Classical and quantum chaos in atom optics

    International Nuclear Information System (INIS)

    Saif, Farhan

    2005-01-01

    The interaction of an atom with an electro-magnetic field is discussed in the presence of a time periodic external modulating force. It is explained that a control on atom by electro-magnetic fields helps to design the quantum analog of classical optical systems. In these atom optical systems chaos may appear at the onset of external fields. The classical and quantum chaotic dynamics is discussed, in particular in an atom optics Fermi accelerator. It is found that the quantum dynamics exhibits dynamical localization and quantum recurrences

  20. X-ray diffraction from ideal mosaic crystals in external fields of certain types. I. Atomic displacements and the corresponding diffraction patterns

    International Nuclear Information System (INIS)

    Treushnikov, E.N.

    2000-01-01

    The problem of the theoretical description of X-ray diffraction from ideal mosaic crystals under the effect of various external fields has been formulated. Electric, magnetic, electromagnetic, and acoustic perturbations are considered. The atomic displacements in crystals under the effect of external fields and the types of the corresponding diffraction patterns are analyzed for various types of perturbations. The crystal classes are determined in which atomic displacements can be recorded experimentally. Diffraction patterns formed under the effect of various external factors are considered on the basis of the derived dependence of the structure factor on the characteristics of an applied force field

  1. Magnetic-field-driven localization of light in a cold-atom gas.

    Science.gov (United States)

    Skipetrov, S E; Sokolov, I M

    2015-02-06

    We discover a transition from extended to localized quasimodes for light in a gas of immobile two-level atoms in a magnetic field. The transition takes place either upon increasing the number density of atoms in a strong field or upon increasing the field at a high enough density. It has many characteristic features of a disorder-driven (Anderson) transition but is strongly influenced by near-field interactions between atoms and the anisotropy of the atomic medium induced by the magnetic field.

  2. Dynamics of an atomic wave packet in a standing-wave cavity field: A cavity-assisted single-atom detection

    International Nuclear Information System (INIS)

    Chough, Young-Tak; Nha, Hyunchul; Kim, Sang Wook; An, Kyungwon; Youn, Sun-Hyun

    2002-01-01

    We investigate the single-atom detection system using an optical standing-wave cavity, from the viewpoint of the quantized center-of-mass motion of the atomic wave packet. We show that since the atom-field coupling strength depends upon the overlap integral of the atomic wave packet and the field mode function, the effect of the wave-packet spreading via the momentum exchange process brings about a significant effect in the detection efficiency. We find that, as a result, the detection efficiency is not sensitive to the individual atomic trajectory for reasonably slow atoms. We also address an interesting phenomenon of the atomic wave-packet splitting occurring when an atom passes through a node of the cavity field

  3. Midinfrared absorption measured at a lambda/400 resolution with an atomic force microscope.

    Science.gov (United States)

    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.

  4. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    Energy Technology Data Exchange (ETDEWEB)

    Markutsya, Sergiy [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Lamm, Monica H., E-mail: mhlamm@iastate.edu [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011 (United States)

    2014-11-07

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  5. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    International Nuclear Information System (INIS)

    Markutsya, Sergiy; Lamm, Monica H.

    2014-01-01

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems

  6. Creation and recovery of a W(111) single atom gas field ion source

    International Nuclear Information System (INIS)

    Pitters, Jason L.; Urban, Radovan; Wolkow, Robert A.

    2012-01-01

    Tungsten single atom tips have been prepared from a single crystal W(111) oriented wire using the chemical assisted field evaporation and etching method. Etching to a single atom tip occurs through a symmetric structure and leads to a predictable last atom unlike etching with polycrystalline tips. The single atom tip formation procedure is shown in an atom by atom removal process. Rebuilds of single atom tips occur on the same crystalline axis as the original tip such that ion emission emanates along a fixed direction for all tip rebuilds. This preparation method could be utilized and developed to prepare single atom tips for ion source development.

  7. Entropy for the Quantized Field in the Atom-Field Interaction: Initial Thermal Distribution

    Directory of Open Access Journals (Sweden)

    Luis Amilca Andrade-Morales

    2016-09-01

    Full Text Available We study the entropy of a quantized field in interaction with a two-level atom (in a pure state when the field is initially in a mixture of two number states. We then generalise the result for a thermal state; i.e., an (infinite statistical mixture of number states. We show that for some specific interaction times, the atom passes its purity to the field and therefore the field entropy decreases from its initial value.

  8. A novel proof of the DFT formula for the interatomic force field of Molecular Dynamics

    International Nuclear Information System (INIS)

    Morante, S.; Rossi, G.C.

    2017-01-01

    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.

  9. A novel proof of the DFT formula for the interatomic force field of Molecular Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Morante, S., E-mail: morante@roma2.infn.it [Dipartimento di Fisica, Università di Roma, “ Tor Vergata ”, INFN, Sezione di Roma 2, Via della Ricerca Scientifica - 00133 Roma (Italy); Rossi, G.C., E-mail: rossig@roma2.infn.it [Dipartimento di Fisica, Università di Roma, “ Tor Vergata ”, INFN, Sezione di Roma 2, Via della Ricerca Scientifica - 00133 Roma (Italy); Centro Fermi-Museo Storico della Fisica e Centro Studi e Ricerche E. Fermi, Compendio del Viminale, Piazza del Viminale 1, I-00184 Rome (Italy)

    2017-02-15

    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.

  10. Effects of Force Field Selection on the Computational Ranking of MOFs for CO2 Separations.

    Science.gov (United States)

    Dokur, Derya; Keskin, Seda

    2018-02-14

    Metal-organic frameworks (MOFs) have been considered as highly promising materials for adsorption-based CO 2 separations. The number of synthesized MOFs has been increasing very rapidly. High-throughput molecular simulations are very useful to screen large numbers of MOFs in order to identify the most promising adsorbents prior to extensive experimental studies. Results of molecular simulations depend on the force field used to define the interactions between gas molecules and MOFs. Choosing the appropriate force field for MOFs is essential to make reliable predictions about the materials' performance. In this work, we performed two sets of molecular simulations using the two widely used generic force fields, Dreiding and UFF, and obtained adsorption data of CO 2 /H 2 , CO 2 /N 2 , and CO 2 /CH 4 mixtures in 100 different MOF structures. Using this adsorption data, several adsorbent evaluation metrics including selectivity, working capacity, sorbent selection parameter, and percent regenerability were computed for each MOF. MOFs were then ranked based on these evaluation metrics, and top performing materials were identified. We then examined the sensitivity of the MOF rankings to the force field type. Our results showed that although there are significant quantitative differences between some adsorbent evaluation metrics computed using different force fields, rankings of the top MOF adsorbents for CO 2 separations are generally similar: 8, 8, and 9 out of the top 10 most selective MOFs were found to be identical in the ranking for CO 2 /H 2 , CO 2 /N 2 , and CO 2 /CH 4 separations using Dreiding and UFF. We finally suggested a force field factor depending on the energy parameters of atoms present in the MOFs to quantify the robustness of the simulation results to the force field selection. This easily computable factor will be highly useful to determine whether the results are sensitive to the force field type or not prior to performing computationally demanding

  11. Atomic force microscopy of starch systems.

    Science.gov (United States)

    Zhu, Fan

    2017-09-22

    Atomic force microscopy (AFM) generates information on topography, adhesion, and elasticity of sample surface by touching with a tip. Under suitable experimental settings, AFM can image biopolymers of few nanometers. Starch is a major food and industrial component. AFM has been used to probe the morphology, properties, modifications, and interactions of starches from diverse botanical origins at both micro- and nano-structural levels. The structural information obtained by AFM supports the blocklet structure of the granules, and provides qualitative and quantitative basis for some physicochemical properties of diverse starch systems. It becomes evident that AFM can complement other microscopic techniques to provide novel structural insights for starch systems.

  12. Bi-harmonic cantilever design for improved measurement sensitivity in tapping-mode atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Loganathan, Muthukumaran; Bristow, Douglas A., E-mail: dbristow@mst.edu [Department of Mechanical and Aerospace Engineering, Missouri University of Science and Technology, Rolla, Missouri 65401 (United States)

    2014-04-15

    This paper presents a method and cantilever design for improving the mechanical measurement sensitivity in the atomic force microscopy (AFM) tapping mode. The method uses two harmonics in the drive signal to generate a bi-harmonic tapping trajectory. Mathematical analysis demonstrates that the wide-valley bi-harmonic tapping trajectory is as much as 70% more sensitive to changes in the sample topography than the standard single-harmonic trajectory typically used. Although standard AFM cantilevers can be driven in the bi-harmonic tapping trajectory, they require large forcing at the second harmonic. A design is presented for a bi-harmonic cantilever that has a second resonant mode at twice its first resonant mode, thereby capable of generating bi-harmonic trajectories with small forcing signals. Bi-harmonic cantilevers are fabricated by milling a small cantilever on the interior of a standard cantilever probe using a focused ion beam. Bi-harmonic drive signals are derived for standard cantilevers and bi-harmonic cantilevers. Experimental results demonstrate better than 30% improvement in measurement sensitivity using the bi-harmonic cantilever. Images obtained through bi-harmonic tapping exhibit improved sharpness and surface tracking, especially at high scan speeds and low force fields.

  13. Bi-harmonic cantilever design for improved measurement sensitivity in tapping-mode atomic force microscopy.

    Science.gov (United States)

    Loganathan, Muthukumaran; Bristow, Douglas A

    2014-04-01

    This paper presents a method and cantilever design for improving the mechanical measurement sensitivity in the atomic force microscopy (AFM) tapping mode. The method uses two harmonics in the drive signal to generate a bi-harmonic tapping trajectory. Mathematical analysis demonstrates that the wide-valley bi-harmonic tapping trajectory is as much as 70% more sensitive to changes in the sample topography than the standard single-harmonic trajectory typically used. Although standard AFM cantilevers can be driven in the bi-harmonic tapping trajectory, they require large forcing at the second harmonic. A design is presented for a bi-harmonic cantilever that has a second resonant mode at twice its first resonant mode, thereby capable of generating bi-harmonic trajectories with small forcing signals. Bi-harmonic cantilevers are fabricated by milling a small cantilever on the interior of a standard cantilever probe using a focused ion beam. Bi-harmonic drive signals are derived for standard cantilevers and bi-harmonic cantilevers. Experimental results demonstrate better than 30% improvement in measurement sensitivity using the bi-harmonic cantilever. Images obtained through bi-harmonic tapping exhibit improved sharpness and surface tracking, especially at high scan speeds and low force fields.

  14. Imaging and manipulation of single viruses by atomic force microscopy

    NARCIS (Netherlands)

    Baclayon, M.; Wuite, G. J. L.; Roos, W. H.

    2010-01-01

    The recent developments in virus research and the application of functional viral particles in nanotechnology and medicine rely on sophisticated imaging and manipulation techniques at nanometre resolution in liquid, air and vacuum. Atomic force microscopy (AFM) is a tool that combines these

  15. Transition States from Empirical Force Fields

    DEFF Research Database (Denmark)

    Jensen, Frank; Norrby, Per-Ola

    2003-01-01

    This is an overview of the use of empirical force fields in the study of reaction mechanisms. EVB-type methods (including RFF and MCMM) produce full reaction surfaces by mixing, in the simplest case, known force fields describing reactants and products. The SEAM method instead locates approximate...

  16. The effects of atomic force microscopy upon nominated living cells

    Energy Technology Data Exchange (ETDEWEB)

    O' Hagan, Barry Michael Gerard [School of Biomedical Sciences, University of Ulster, Cromore Road, Coleraine, County Londonderry, BT52 1SA (United Kingdom)]. E-mail: bmg.ohagan@ulstser.ac.uk; Doyle, Peter [Unilever Research, Port Sunlight, The Wirral, Merseyside (United Kingdom); Allen, James M. [School of Biomedical Sciences, University of Ulster, Cromore Road, Coleraine, County Londonderry, BT52 1SA (United Kingdom); Sutton, Kerry [School of Biomedical Sciences, University of Ulster, Cromore Road, Coleraine, County Londonderry, BT52 1SA (United Kingdom); McKerr, George [School of Biomedical Sciences, University of Ulster, Cromore Road, Coleraine, County Londonderry, BT52 1SA (United Kingdom)

    2004-12-15

    This work describes a system for precise re-location of cells within a monolayer after atomic force imaging. As we know little about probe interaction with soft biological surfaces any corroborative evidence is of great importance. For example, it is of paramount importance in living cell force microscopy that interrogated cells can be re-located and imaged by other corroborative technologies. Methodologies expressed here have shown that non-invasive force parameters can be established for specific cell types. Additionally, we show that the same sample can be transferred reliably to an SEM. Results here indicate that further work with live cells should initially establish appropriate prevailing force parameters and that cell damage should be checked for before and after an imaging experiment.

  17. The effects of atomic force microscopy upon nominated living cells

    International Nuclear Information System (INIS)

    O'Hagan, Barry Michael Gerard; Doyle, Peter; Allen, James M.; Sutton, Kerry; McKerr, George

    2004-01-01

    This work describes a system for precise re-location of cells within a monolayer after atomic force imaging. As we know little about probe interaction with soft biological surfaces any corroborative evidence is of great importance. For example, it is of paramount importance in living cell force microscopy that interrogated cells can be re-located and imaged by other corroborative technologies. Methodologies expressed here have shown that non-invasive force parameters can be established for specific cell types. Additionally, we show that the same sample can be transferred reliably to an SEM. Results here indicate that further work with live cells should initially establish appropriate prevailing force parameters and that cell damage should be checked for before and after an imaging experiment

  18. NATO Advanced Study Institute on Atoms in Strong Fields

    CERN Document Server

    Clark, Charles; Nayfeh, Munir

    1990-01-01

    This book collects the lectures given at the NATO Advanced Study Institute on "Atoms in Strong Fields", which took place on the island of Kos, Greece, during the two weeks of October 9-21,1988. The designation "strong field" applies here to an external electromagnetic field that is sufficiently strong to cause highly nonlinear alterations in atomic or molecular struc­ ture and dynamics. The specific topics treated in this volume fall into two general cater­ gories, which are those for which strong field effects can be studied in detail in terrestrial laboratories: the dynamics of excited states in static or quasi-static electric and magnetic fields; and the interaction of atoms and molecules with intense laser radiation. In both areas there exist promising opportunities for research of a fundamental nature. An electric field of even a few volts per centimeter can be very strong on the atom­ ic scale, if it acts upon a weakly bound state. The study of Rydberg states with high reso­ lution laser spectroscop...

  19. Two-dimensional atom localization via two standing-wave fields in a four-level atomic system

    International Nuclear Information System (INIS)

    Zhang Hongtao; Wang Hui; Wang Zhiping

    2011-01-01

    We propose a scheme for the two-dimensional (2D) localization of an atom in a four-level Y-type atomic system. By applying two orthogonal standing-wave fields, the atoms can be localized at some special positions, leading to the formation of sub-wavelength 2D periodic spatial distributions. The localization peak position and number as well as the conditional position probability can be controlled by the intensities and detunings of optical fields.

  20. Atomic excitation and acceleration in strong laser fields

    International Nuclear Information System (INIS)

    Zimmermann, H; Eichmann, U

    2016-01-01

    Atomic excitation in the tunneling regime of a strong-field laser–matter interaction has been recently observed. It is conveniently explained by the concept of frustrated tunneling ionization (FTI), which naturally evolves from the well-established tunneling picture followed by classical dynamics of the electron in the combined laser field and Coulomb field of the ionic core. Important predictions of the FTI model such as the n distribution of Rydberg states after strong-field excitation and the dependence on the laser polarization have been confirmed in experiments. The model also establishes a sound basis to understand strong-field acceleration of neutral atoms in strong laser fields. The experimental observation has become possible recently and initiated a variety of experiments such as atomic acceleration in an intense standing wave and the survival of Rydberg states in strong laser fields. Furthermore, the experimental investigations on strong-field dissociation of molecules, where neutral excited fragments after the Coulomb explosion of simple molecules have been observed, can be explained. In this review, we introduce the subject and give an overview over relevant experiments supplemented by new results. (paper)

  1. Manipulation and soldering of carbon nanotubes using atomic force microscope

    International Nuclear Information System (INIS)

    Kashiwase, Yuta; Ikeda, Takayuki; Oya, Takahide; Ogino, Toshio

    2008-01-01

    Manipulation of carbon nanotubes (CNTs) by an atomic force microscope (AFM) and soldering of CNTs using Fe oxide nanoparticles are described. We succeeded to separate a CNT bundle into two CNTs or CNT bundles, to move the separated CNT to a desirable position, and to bind it to another bundle. For the accurate manipulation, load of the AFM cantilever and frequency of the scan were carefully selected. We soldered two CNTs using an Fe oxide nanoparticle prepared from a ferritin molecule. The adhesion forces between the soldered CNTs were examined by an AFM and it was found that the CNTs were bound, though the binding force was not strong

  2. Application of the nuclear field theory to monopole interactions which include all the vertices of a general force

    International Nuclear Information System (INIS)

    Bes, D.R.; Dussel, G.G.; Liotta, R.J.; Sofia, H.M.; Broglia, R.A.

    1976-01-01

    The field treatment is applied to the monopole pairing and monopole particle-hole interactions in a two-level model. All the vertices of realistic interactions appear, and the problems treated here have most of the complexities of real nuclei. Yet, the model remains sufficiently simple, so that a close comparison with the results of a (conventional) treatment in which only the fermion degrees of freedom are considered is possible. The applicability to actual physical situations appears to be feasible, both for schematic or realistic forces. The advantage of including the exchange components of the interaction in the construction of the phonon is discussed. (Auth.)

  3. Noise squeezing of fields that bichromatically excite atoms in a cavity.

    Science.gov (United States)

    Li, Lingchao; Hu, Xiangming; Rao, Shi; Xu, Jun

    2016-11-14

    It is well known that bichromatic excitation on one common transition can tune the emission or absorption spectra of atoms due to the modulation frequency dependent non-linearities. However little attention has been focused on the quantum dynamics of fields under bichromatic excitation. Here we present dissipative effects on noise correlations of fields in bichromatic interactions with atoms in cavities. We first consider an ensemble of two-level atoms that interacts with the two cavity fields of different frequencies and considerable amplitudes. By transferring the atom-field nonlinearities to the dressed atoms we separate out the dissipative interactions of Bogoliubov modes with the dressed atoms. The Bogoliubov mode dissipation establishes stable two-photon processes of two involved fields and therefore leads to two-mode squeezing. As a generalization, we then consider an ensemble of three-level Λ atoms for cascade bichromatic interactions. We extract the Bogoliubov-like four-mode interactions, which establish a quadrilateral of the two-photon processes of four involved fields and thus result in four-mode squeezing.

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

    Directory of Open Access Journals (Sweden)

    Carlos Sabater

    2015-12-01

    Full Text Available 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.

  5. Multiphoton processes for atoms in intense electromagnetic fields

    Energy Technology Data Exchange (ETDEWEB)

    Collins, L.A.; Abdallah, J.; Csanak, G.

    1995-12-31

    Lasers from table-top to giant ICF facilities that produce intense electromagnetic fields (10{sup 14}-10{sup 21} W/cm{sup 2}) have become important tools in probing the intricate nature of matter-radiation interactions. At such intensities, the laser field equals or exceeds that which binds electrons to an atom or molecule, and a new realm of physics opens in which perturbation theory may no longer suffice. We are developing several sophisticated techniques for treating atoms in such a regime, concentrating on two-photon X-ray absorption in intermediate-weight atoms and on laser-assisted electron-atom collisions. We perform most calculations in a time-independent frame in which field-free scattering formalisms can be invoked. We also investigate time-dependent methods in order to study transient effects. This is the final report of a three-year Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL).

  6. Chemical bond imaging using higher eigenmodes of tuning fork sensors in atomic force microscopy

    Science.gov (United States)

    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.

  7. Nanoscale imaging of the growth and division of bacterial cells on planar substrates with the atomic force microscope

    Energy Technology Data Exchange (ETDEWEB)

    Van Der Hofstadt, M. [Institut de Bioenginyeria de Catalunya (IBEC), C/ Baldiri i Reixac 11-15, 08028 Barcelona (Spain); Hüttener, M.; Juárez, A. [Institut de Bioenginyeria de Catalunya (IBEC), C/ Baldiri i Reixac 11-15, 08028 Barcelona (Spain); Departament de Microbiologia, Universitat de Barcelona, Avinguda Diagonal 645, 08028 Barcelona (Spain); Gomila, G., E-mail: ggomila@ibecbarcelona.eu [Institut de Bioenginyeria de Catalunya (IBEC), C/ Baldiri i Reixac 11-15, 08028 Barcelona (Spain); Departament d' Electronica, Universitat de Barcelona, C/ Marti i Franqués 1, 08028 Barcelona (Spain)

    2015-07-15

    With the use of the atomic force microscope (AFM), the Nanomicrobiology field has advanced drastically. Due to the complexity of imaging living bacterial processes in their natural growing environments, improvements have come to a standstill. Here we show the in situ nanoscale imaging of the growth and division of single bacterial cells on planar substrates with the atomic force microscope. To achieve this, we minimized the lateral shear forces responsible for the detachment of weakly adsorbed bacteria on planar substrates with the use of the so called dynamic jumping mode with very soft cantilever probes. With this approach, gentle imaging conditions can be maintained for long periods of time, enabling the continuous imaging of the bacterial cell growth and division, even on planar substrates. Present results offer the possibility to observe living processes of untrapped bacteria weakly attached to planar substrates. - Highlights: • Gelatine coatings used to weakly attach bacterial cells onto planar substrates. • Use of the dynamic jumping mode as a non-perturbing bacterial imaging mode. • Nanoscale resolution imaging of unperturbed single living bacterial cells. • Growth and division of single bacteria cells on planar substrates observed.

  8. Manipulating Neutral Atoms in Chip-Based Magnetic Traps

    Science.gov (United States)

    Aveline, David; Thompson, Robert; Lundblad, Nathan; Maleki, Lute; Yu, Nan; Kohel, James

    2009-01-01

    Several techniques for manipulating neutral atoms (more precisely, ultracold clouds of neutral atoms) in chip-based magnetic traps and atomic waveguides have been demonstrated. Such traps and waveguides are promising components of future quantum sensors that would offer sensitivities much greater than those of conventional sensors. Potential applications include gyroscopy and basic research in physical phenomena that involve gravitational and/or electromagnetic fields. The developed techniques make it possible to control atoms with greater versatility and dexterity than were previously possible and, hence, can be expected to contribute to the value of chip-based magnetic traps and atomic waveguides. The basic principle of these techniques is to control gradient magnetic fields with suitable timing so as to alter a trap to exert position-, velocity-, and/or time-dependent forces on atoms in the trap to obtain desired effects. The trap magnetic fields are generated by controlled electric currents flowing in both macroscopic off-chip electromagnet coils and microscopic wires on the surface of the chip. The methods are best explained in terms of examples. Rather than simply allowing atoms to expand freely into an atomic waveguide, one can give them a controllable push by switching on an externally generated or a chip-based gradient magnetic field. This push can increase the speed of the atoms, typically from about 5 to about 20 cm/s. Applying a non-linear magnetic-field gradient exerts different forces on atoms in different positions a phenomenon that one can exploit by introducing a delay between releasing atoms into the waveguide and turning on the magnetic field.

  9. Application of atomic force microscopy to the study of natural and model soil particles.

    Science.gov (United States)

    Cheng, S; Bryant, R; Doerr, S H; Rhodri Williams, P; Wright, C J

    2008-09-01

    The structure and surface chemistry of soil particles has extensive impact on many bulk scale properties and processes of soil systems and consequently the environments that they support. There are a number of physiochemical mechanisms that operate at the nanoscale which affect the soil's capability to maintain native vegetation and crops; this includes soil hydrophobicity and the soil's capacity to hold water and nutrients. The present study used atomic force microscopy in a novel approach to provide unique insight into the nanoscale properties of natural soil particles that control the physiochemical interaction of material within the soil column. There have been few atomic force microscopy studies of soil, perhaps a reflection of the heterogeneous nature of the system. The present study adopted an imaging and force measurement research strategy that accounted for the heterogeneity and used model systems to aid interpretation. The surface roughness of natural soil particles increased with depth in the soil column a consequence of the attachment of organic material within the crevices of the soil particles. The roughness root mean square calculated from ten 25 microm(2) images for five different soil particles from a Netherlands soil was 53.0 nm, 68.0 nm, 92.2 nm and 106.4 nm for the respective soil depths of 0-10 cm, 10-20 cm, 20-30 cm and 30-40 cm. A novel analysis method of atomic force microscopy phase images based on phase angle distribution across a surface was used to interpret the nanoscale distribution of organic material attached to natural and model soil particles. Phase angle distributions obtained from phase images of model surfaces were found to be bimodal, indicating multiple layers of material, which changed with the concentration of adsorbed humic acid. Phase angle distributions obtained from phase images of natural soil particles indicated a trend of decreasing surface coverage with increasing depth in the soil column. This was consistent with

  10. Effectiveness of Modal Decomposition for Tapping Atomic Force Microscopy Microcantilevers in Liquid Environment.

    Science.gov (United States)

    Kim, Il Kwang; Lee, Soo Il

    2016-05-01

    The modal decomposition of tapping mode atomic force microscopy microcantilevers in liquid environments was studied experimentally. Microcantilevers with different lengths and stiffnesses and two sample surfaces with different elastic moduli were used in the experiment. The response modes of the microcantilevers were extracted as proper orthogonal modes through proper orthogonal decomposition. Smooth orthogonal decomposition was used to estimate the resonance frequency directly. The effects of the tapping setpoint and the elastic modulus of the sample under test were examined in terms of their multi-mode responses with proper orthogonal modes, proper orthogonal values, smooth orthogonal modes and smooth orthogonal values. Regardless of the stiffness of the microcantilever under test, the first mode was dominant in tapping mode atomic force microscopy under normal operating conditions. However, at lower tapping setpoints, the flexible microcantilever showed modal distortion and noise near the tip when tapping on a hard sample. The stiff microcantilever had a higher mode effect on a soft sample at lower tapping setpoints. Modal decomposition for tapping mode atomic force microscopy can thus be used to estimate the characteristics of samples in liquid environments.

  11. A novel self-sensing technique for tapping-mode atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ruppert, Michael G.; Moheimani, S. O. Reza [The University of Newcastle, University Drive, Callaghan NSW 2308 (Australia)

    2013-12-15

    This work proposes a novel self-sensing tapping-mode atomic force microscopy operation utilizing charge measurement. A microcantilever coated with a single piezoelectric layer is simultaneously used for actuation and deflection sensing. The cantilever can be batch fabricated with existing micro electro mechanical system processes. The setup enables the omission of the optical beam deflection technique which is commonly used to measure the cantilever oscillation amplitude. Due to the high amount of capacitive feedthrough in the measured charge signal, a feedforward control technique is employed to increase the dynamic range from less than 1 dB to approximately 35 dB. Experiments show that the conditioned charge signal achieves excellent signal-to-noise ratio and can therefore be used as a feedback signal for atomic force microscopy imaging.

  12. Atomic force microscopy observation of lipopolysaccharide-induced cardiomyocyte cytoskeleton reorganization.

    Science.gov (United States)

    Wang, Liqun; Chen, Tangting; Zhou, Xiang; Huang, Qiaobing; Jin, Chunhua

    2013-08-01

    We applied atomic force microscopy (AFM) to observe lipopolysaccharide (LPS)-induced intracellular cytoskeleton reorganization in primary cardiomyocytes from neonatal mouse. The nonionic detergent Triton X-100 was used to remove the membrane, soluble proteins, and organelles from the cell. The remaining cytoskeleton can then be directly visualized by AFM. Using three-dimensional technique of AFM, we were able to quantify the changes of cytoskeleton by the "density" and total "volume" of the cytoskeleton fibers. Compared to the control group, the density of cytoskeleton was remarkably decreased and the volume of cytoskeleton was significantly increased after LPS treatment, which suggests that LPS may induce the cytoskeleton reorganization and change the cardiomyocyte morphology. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Measuring the elasticity of plant cells with atomic force microscopy.

    Science.gov (United States)

    Braybrook, Siobhan A

    2015-01-01

    The physical properties of biological materials impact their functions. This is most evident in plants where the cell wall contains each cell's contents and connects each cell to its neighbors irreversibly. Examining the physical properties of the plant cell wall is key to understanding how plant cells, tissues, and organs grow and gain the shapes important for their respective functions. Here, we present an atomic force microscopy-based nanoindentation method for examining the elasticity of plant cells at the subcellular, cellular, and tissue level. We describe the important areas of experimental design to be considered when planning and executing these types of experiments and provide example data as illustration. Copyright © 2015 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2012-01-10

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

  15. Force-free field model of ball lightning

    International Nuclear Information System (INIS)

    Tsui, K.H.

    2001-01-01

    Due to the nature that the force-free magnetic field, whose current carried by the conducting plasma is everywhere parallel to the magnetic field it generates, is the minimum energy configuration under the constraint of magnetic helicity conservation, ball lightning is considered as a self-organized phenomenon with a plasma fireball immersed in a spherical force-free magnetic field. Since this field does not exert force on the plasma, the plasma pressure, by itself, is in equilibrium with the surrounding environment, and the force-free magnetic field can take on any value without affecting the plasma. Due to this second feature, singular solutions of the magnetic field that are otherwise excluded are allowed, which enable a large amount of energy to be stored to sustain the ball lightning. The singularity is truncated only by the physical limit of current density that a plasma can carry. Scaling the customary soccer-size fireball to larger dimensions could account for day and night sightings of luminous objects in the sky

  16. Atomic force microscope with integrated optical microscope for biological applications

    NARCIS (Netherlands)

    Putman, Constant A.J.; Putman, C.A.J.; van der Werf, Kees; de Grooth, B.G.; van Hulst, N.F.; Segerink, Franciscus B.; Greve, Jan

    1992-01-01

    Since atomic force microscopy (AFM) is capable of imaging nonconducting surfaces, the technique holds great promises for high‐resolution imaging of biological specimens. A disadvantage of most AFMs is the fact that the relatively large sample surface has to be scanned multiple times to pinpoint a

  17. „New approaches to atomic force microscope lithography on silicon"

    DEFF Research Database (Denmark)

    Birkelund, Karen; Thomsen, Erik Vilain; Rasmussen, Jan Pihl

    1997-01-01

    We have investigated new approaches to the formation of conducting nanowires on crystalline silicon surfaces using atomic force microscope (AFM) lithography. To increase processing speed and reduce wear of the AFM tip, large-scale structures are formed with a direct laser write setup, while the AFM...

  18. Imaging of RNA in situ hybridization by atomic force microscopy

    NARCIS (Netherlands)

    Kalle, W.H.J.; Macville, M.V.E.; van de Corput, M.P.C.; de Grooth, B.G.; Tanke, H.J.; Raap, A.K.

    In this study we investigated the possibility of imaging internal cellular molecules after cytochemical detection with atomic force microscopy (AFM). To this end, rat 9G and HeLa cells were hybridized with haptenized probes for 28S ribosomal RNA, human elongation factor mRNA and cytomegalovirus

  19. Photon scanning tunneling microscope in combination with a force microscope

    NARCIS (Netherlands)

    Moers, M.H.P.; Moers, M.H.P.; Tack, R.G.; van Hulst, N.F.; Bölger, B.; Bölger, B.

    1994-01-01

    The simultaneous operation of a photon scanning tunneling microscope with an atomic force microscope is presented. The use of standard atomic force silicon nitride cantilevers as near-field optical probes offers the possibility to combine the two methods. Vertical forces and torsion are detected

  20. Surface features on Sahara soil dust particles made visible by atomic force microscope (AFM) phase images

    OpenAIRE

    G. Helas; M. O. Andreae

    2008-01-01

    We show that atomic force microscopy (AFM) phase images can reveal surface features of soil dust particles, which are not evident using other microscopic methods. The non-contact AFM method is able to resolve topographical structures in the nanometer range as well as to uncover repulsive atomic forces and attractive van der Waals' forces, and thus gives insight to surface properties. Though the method does not allow quantitative assignment in terms of chemical compound description, it clearly...

  1. Characterizing absolute piezoelectric microelectromechanical system displacement using an atomic force microscope

    International Nuclear Information System (INIS)

    Evans, J.; Chapman, S.

    2014-01-01

    Piezoresponse Force Microscopy (PFM) is a popular tool for the study of ferroelectric and piezoelectric materials at the nanometer level. Progress in the development of piezoelectric MEMS fabrication is highlighting the need to characterize absolute displacement at the nanometer and Ångstrom scales, something Atomic Force Microscopy (AFM) might do but PFM cannot. Absolute displacement is measured by executing a polarization measurement of the ferroelectric or piezoelectric capacitor in question while monitoring the absolute vertical position of the sample surface with a stationary AFM cantilever. Two issues dominate the execution and precision of such a measurement: (1) the small amplitude of the electrical signal from the AFM at the Ångstrom level and (2) calibration of the AFM. The authors have developed a calibration routine and test technique for mitigating the two issues, making it possible to use an atomic force microscope to measure both the movement of a capacitor surface as well as the motion of a micro-machine structure actuated by that capacitor. The theory, procedures, pitfalls, and results of using an AFM for absolute piezoelectric measurement are provided

  2. Characterizing absolute piezoelectric microelectromechanical system displacement using an atomic force microscope

    Energy Technology Data Exchange (ETDEWEB)

    Evans, J., E-mail: radiant@ferrodevices.com; Chapman, S., E-mail: radiant@ferrodevices.com [Radiant Technologies, Inc., 2835C Pan American Fwy NE, Albuquerque, New Mexico 87107 (United States)

    2014-08-14

    Piezoresponse Force Microscopy (PFM) is a popular tool for the study of ferroelectric and piezoelectric materials at the nanometer level. Progress in the development of piezoelectric MEMS fabrication is highlighting the need to characterize absolute displacement at the nanometer and Ångstrom scales, something Atomic Force Microscopy (AFM) might do but PFM cannot. Absolute displacement is measured by executing a polarization measurement of the ferroelectric or piezoelectric capacitor in question while monitoring the absolute vertical position of the sample surface with a stationary AFM cantilever. Two issues dominate the execution and precision of such a measurement: (1) the small amplitude of the electrical signal from the AFM at the Ångstrom level and (2) calibration of the AFM. The authors have developed a calibration routine and test technique for mitigating the two issues, making it possible to use an atomic force microscope to measure both the movement of a capacitor surface as well as the motion of a micro-machine structure actuated by that capacitor. The theory, procedures, pitfalls, and results of using an AFM for absolute piezoelectric measurement are provided.

  3. MIDAS: Lessons learned from the first spaceborne atomic force microscope

    Science.gov (United States)

    Bentley, Mark Stephen; Arends, Herman; Butler, Bart; Gavira, Jose; Jeszenszky, Harald; Mannel, Thurid; Romstedt, Jens; Schmied, Roland; Torkar, Klaus

    2016-08-01

    The Micro-Imaging Dust Analysis System (MIDAS) atomic force microscope (AFM) onboard the Rosetta orbiter was the first such instrument launched into space in 2004. Designed only a few years after the technique was invented, MIDAS is currently orbiting comet 67P Churyumov-Gerasimenko and producing the highest resolution 3D images of cometary dust ever made in situ. After more than a year of continuous operation much experience has been gained with this novel instrument. Coupled with operations of the Flight Spare and advances in terrestrial AFM a set of "lessons learned" has been produced, cumulating in recommendations for future spaceborne atomic force microscopes. The majority of the design could be reused as-is, or with incremental upgrades to include more modern components (e.g. the processor). Key additional recommendations are to incorporate an optical microscope to aid the search for particles and image registration, to include a variety of cantilevers (with different spring constants) and a variety of tip geometries.

  4. Electron-atom collisions in a laser field

    International Nuclear Information System (INIS)

    Ehlotzky, F.

    1998-01-01

    The present work is a report on recent progress made in our understanding of electron-atom collisions in a laser field. To some extent it is a continuation of a previous review covering a somewhat larger subject (Can. J. Phys. 63 (1985)). We shall discuss the present status of investigations in this field from the theoretical as well as experimental point of view but most of the report will be devoted to an analysis of the various approximation schemes used at present in this field to describe the different aspects of laser-assisted electron-atom interactions. As the table of contents shows, most of the work done so far is treating the atom as a spectator, described by a potential and only very little has been achieved over the years to include the atomic structure into consideration since the inclusion of these structure effects poses considerable computational problems. Since, for example, multiphoton ionization and its inverse process laser-assisted recombination may be considered as one half of a scattering process, it is quite natural that some of the theoretical techniques described here are also of interest for the treatment of other multiphoton processes not considered here since there are several other recent reviews available on these topics. (orig.)

  5. Theoretical Investigation of Hydrogen Adsorption and Dissociation on Iron and Iron Carbide Surfaces Using the ReaxFF Reactive Force Field Method

    Energy Technology Data Exchange (ETDEWEB)

    Zou, Chenyu; van Duin, Adri C.T.; Sorescu, Dan C.

    2012-06-01

    We have developed a ReaxFF reactive force field to describe hydrogen adsorption and dissociation on iron and iron carbide surfaces relevant for simulation of Fischer–Tropsch (FT) synthesis on iron catalysts. This force field enables large system (>>1000 atoms) simulations of hydrogen related reactions with iron. The ReaxFF force field parameters are trained against a substantial amount of structural and energetic data including the equations of state and heats of formation of iron and iron carbide related materials, as well as hydrogen interaction with iron surfaces and different phases of bulk iron. We have validated the accuracy and applicability of ReaxFF force field by carrying out molecular dynamics simulations of hydrogen adsorption, dissociation and recombination on iron and iron carbide surfaces. The barriers and reaction energies for molecular dissociation on these two types of surfaces have been compared and the effect of subsurface carbon on hydrogen interaction with iron surface is evaluated. We found that existence of carbon atoms at subsurface iron sites tends to increase the hydrogen dissociation energy barrier on the surface, and also makes the corresponding hydrogen dissociative state relatively more stable compared to that on bare iron. These properties of iron carbide will affect the dissociation rate of H{sub 2} and will retain more surface hydride species, thus influencing the dynamics of the FT synthesis process.

  6. High-frequency multimodal atomic force microscopy

    Directory of Open Access Journals (Sweden)

    Adrian P. Nievergelt

    2014-12-01

    Full Text Available Multifrequency atomic force microscopy imaging has been recently demonstrated as a powerful technique for quickly obtaining information about the mechanical properties of a sample. Combining this development with recent gains in imaging speed through small cantilevers holds the promise of a convenient, high-speed method for obtaining nanoscale topography as well as mechanical properties. Nevertheless, instrument bandwidth limitations on cantilever excitation and readout have restricted the ability of multifrequency techniques to fully benefit from small cantilevers. We present an approach for cantilever excitation and deflection readout with a bandwidth of 20 MHz, enabling multifrequency techniques extended beyond 2 MHz for obtaining materials contrast in liquid and air, as well as soft imaging of delicate biological samples.

  7. Limit on Excitation and Stabilization of Atoms in Intense Optical Laser Fields.

    Science.gov (United States)

    Zimmermann, H; Meise, S; Khujakulov, A; Magaña, A; Saenz, A; Eichmann, U

    2018-03-23

    Atomic excitation in strong optical laser fields has been found to take place even at intensities exceeding saturation. The concomitant acceleration of the atom in the focused laser field has been considered a strong link to, if not proof of, the existence of the so-called Kramers-Henneberger (KH) atom, a bound atomic system in an intense laser field. Recent findings have moved the importance of the KH atom from being purely of theoretical interest toward real world applications; for instance, in the context of laser filamentation. Considering this increasing importance, we explore the limits of strong-field excitation in optical fields, which are basically imposed by ionization through the spatial field envelope and the field propagation.

  8. Microcontroller-driven fluid-injection system for atomic force microscopy.

    Science.gov (United States)

    Kasas, S; Alonso, L; Jacquet, P; Adamcik, J; Haeberli, C; Dietler, G

    2010-01-01

    We present a programmable microcontroller-driven injection system for the exchange of imaging medium during atomic force microscopy. Using this low-noise system, high-resolution imaging can be performed during this process of injection without disturbance. This latter circumstance was exemplified by the online imaging of conformational changes in DNA molecules during the injection of anticancer drug into the fluid chamber.

  9. Invited Article: VEDA: A web-based virtual environment for dynamic atomic force microscopy

    Science.gov (United States)

    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.

  10. Dissolved organic carbon--contaminant interaction descriptors found by 3D force field calculations.

    Science.gov (United States)

    Govers, H A J; Krop, H B; Parsons, J R; Tambach, T; Kubicki, J D

    2002-03-01

    Enthalpies of transfer at 300 K of various partitioning processes were calculated in order to study the suitability of 3D force fields for the calculation of partitioning constants. A 3D fulvic acid (FA) model of dissolved organic carbon (DOC) was built in a MM+ force field using AMI atomic charges and geometrical optimization (GO). 3,5-Dichlorobiphenyl (PCB14), 4,4'-dichlorobiphenyl (PCB15), 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)-ethane (PPDDT) and 2-chloro-4-ethylamino-6-isopropylamino-s-triazine (Atrazine) were inserted into different sites and their interaction energies with FA were calculated. Energies of hydration were calculated and subtracted from FA-contaminant interactions of selected sites. The resulting values for the enthalpies of transfer from water to DOC were 2.8, -1.4, -6.4 and 0.0 kcal/mol for PCB 14, PCB15, PPDDT and Atrazine, respectively. The value of PPDDT compared favorably with the experimental value of -5.0 kcal/mol. Prior to this, the method was studied by the calculation of the enthalpies of vaporization and aqueous solution using various force fields. In the MM + force field GO predicted enthalpies of vaporization deviated by +0.7 (PCB14), +3.6 (PCB15) and -0.7 (PPDDT)kcal/mol from experimental data, whereas enthalpies of aqueous solution deviated by -3.6 (PCB14), +5.8 (PCB15) and +3.7 (PPDDT) kcal/mol. Only for PCB14 the wrong sign of this enthalpy value was predicted. Potential advantages and limitations of the approach were discussed.

  11. Uncertainty quantification in nanomechanical measurements using the atomic force microscope

    Science.gov (United States)

    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...

  12. Protein-Ligand Informatics Force Field (PLIff): Toward a Fully Knowledge Driven "Force Field" for Biomolecular Interactions.

    Science.gov (United States)

    Verdonk, Marcel L; Ludlow, R Frederick; Giangreco, Ilenia; Rathi, Prakash Chandra

    2016-07-28

    The Protein Data Bank (PDB) contains a wealth of data on nonbonded biomolecular interactions. If this information could be distilled down to nonbonded interaction potentials, these would have some key advantages over standard force fields. However, there are some important outstanding issues to address in order to do this successfully. This paper introduces the protein-ligand informatics "force field", PLIff, which begins to address these key challenges ( https://bitbucket.org/AstexUK/pli ). As a result of their knowledge-based nature, the next-generation nonbonded potentials that make up PLIff automatically capture a wide range of interaction types, including special interactions that are often poorly described by standard force fields. We illustrate how PLIff may be used in structure-based design applications, including interaction fields, fragment mapping, and protein-ligand docking. PLIff performs at least as well as state-of-the art scoring functions in terms of pose predictions and ranking compounds in a virtual screening context.

  13. Calibrated atomic force microscope measurements of vickers hardness indentations and tip production and characterisation for scanning tunelling microscope

    DEFF Research Database (Denmark)

    Jensen, Carsten P.

    Calibrated atomic force microscope measurements of vickers hardness indentations and tip production and characterisation for scanning tunelling microscope......Calibrated atomic force microscope measurements of vickers hardness indentations and tip production and characterisation for scanning tunelling microscope...

  14. Analytical relativistic self-consistent-field calculations for atoms

    International Nuclear Information System (INIS)

    Barthelat, J.C.; Pelissier, M.; Durand, P.

    1980-01-01

    A new second-order representation of the Dirac equation is presented. This representation which is exact for a hydrogen atom is applied to approximate analytical self-consistent-field calculations for atoms. Results are given for the rare-gas atoms from helium to radon and for lead. The results compare favorably with numerical Dirac-Hartree-Fock solutions

  15. A new image correction method for live cell atomic force microscopy

    International Nuclear Information System (INIS)

    Shen, Y; Sun, J L; Zhang, A; Hu, J; Xu, L X

    2007-01-01

    During live cell imaging via atomic force microscopy (AFM), the interactions between the AFM probe and the membrane yield distorted cell images. In this work, an image correction method was developed based on the force-distance curve and the modified Hertzian model. The normal loading and lateral forces exerted on the cell membrane by the AFM tip were both accounted for during the scanning. Two assumptions were made in modelling based on the experimental measurements: (1) the lateral force on the endothelial cells was linear to the height; (2) the cell membrane Young's modulus could be derived from the displacement measurement of a normal force curve. Results have shown that the model could be used to recover up to 30% of the actual cell height depending on the loading force. The accuracy of the model was also investigated with respect to the loading force and mechanical property of the cell membrane

  16. Study of adhesion of vertically aligned carbon nanotubes to a substrate by atomic-force microscopy

    Science.gov (United States)

    Ageev, O. A.; Blinov, Yu. F.; Il'ina, M. V.; Il'in, O. I.; Smirnov, V. A.; Tsukanova, O. G.

    2016-02-01

    The adhesion to a substrate of vertically aligned carbon nanotubes (VA CNT) produced by plasmaenhanced chemical vapor deposition has been experimentally studied by atomic-force microscopy in the current spectroscopy mode. The longitudinal deformation of VA CNT by applying an external electric field has been simulated. Based on the results, a technique of determining VA CNT adhesion to a substrate has been developed that is used to measure the adhesion strength of connecting VA CNT to a substrate. The adhesion to a substrate of VA CNT 70-120 nm in diameter varies from 0.55 to 1.19 mJ/m2, and the adhesion force from 92.5 to 226.1 nN. When applying a mechanical load, the adhesion strength of the connecting VA CNT to a substrate is 714.1 ± 138.4 MPa, and the corresponding detachment force increases from 1.93 to 10.33 μN with an increase in the VA CNT diameter. As an external electric field is applied, the adhesion strength is almost doubled and is 1.43 ± 0.29 GPa, and the corresponding detachment force is changed from 3.83 to 20.02 μN. The results can be used in the design of technological processes of formation of emission structures, VA CNT-based elements for vacuum microelectronics and micro- and nanosystem engineering, and also the methods of probe nanodiagnostics of VA CNT.

  17. Automated setpoint adjustment for biological contact mode atomic force microscopy imaging

    International Nuclear Information System (INIS)

    Casuso, Ignacio; Scheuring, Simon

    2010-01-01

    Contact mode atomic force microscopy (AFM) is the most frequently used AFM imaging mode in biology. It is about 5-10 times faster than oscillating mode imaging (in conventional AFM setups), and provides topographs of biological samples with sub-molecular resolution and at a high signal-to-noise ratio. Unfortunately, contact mode imaging is sensitive to the applied force and intrinsic force drift: inappropriate force applied by the AFM tip damages the soft biological samples. We present a methodology that automatically searches for and maintains high resolution imaging forces. We found that the vertical and lateral vibrations of the probe during scanning are valuable signals for the characterization of the actual applied force by the tip. This allows automated adjustment and correction of the setpoint force during an experiment. A system that permanently performs this methodology steered the AFM towards high resolution imaging forces and imaged purple membrane at molecular resolution and live cells at high signal-to-noise ratio for hours without an operator.

  18. Hydrogen atom in intense magnetic field.

    Science.gov (United States)

    Canuto, V.; Kelly, D. C.

    1972-01-01

    The structure of a hydrogen atom situated in an intense magnetic field is investigaged. Three approaches are employed. An elementary Bohr picture establishes a crucial magnetic field strength, H sub a approximately equal to 5 x 10 to the 9th G. Fields in excess of H sub a are intense in that they are able to modify the characteristic atomic scales of length and binding energy. A second approach solves the Schrodinger equation by a combination of variational methods and perturbation theory. It yields analytic expressions for the wave functions and energy eigenvalues. A third approach determines the energy eigenvalues by reducing the Schrodinger equation to a one-dimensional wave equation, which is then solved numerically. Energy eigenvalues are tabulated for field strengths of 2 x 10 to the 10th G and 2 x 10 to the 12th G. It is found that at 2 x 10 to the 12th G the lowest energy eigenvalue is changed from -13.6 to about -180 eV in agreement with previous variational computations.

  19. Single molecule imaging of RNA polymerase II using atomic force microscopy

    International Nuclear Information System (INIS)

    Rhodin, Thor; Fu Jianhua; Umemura, Kazuo; Gad, Mohammed; Jarvis, Suzi; Ishikawa, Mitsuru

    2003-01-01

    An atomic force microscopy (AFM) study of the shape, orientation and surface topology of RNA polymerase II supported on silanized freshly cleaved mica was made. The overall aim is to define the molecular topology of RNA polymerase II in appropriate fluids to help clarify the relationship of conformational features to biofunctionality. A Nanoscope III atomic force microscope was used in the tapping mode with oxide-sharpened (8-10 nm) Si 3 N 4 probes in aqueous zinc chloride buffer. The main structural features observed by AFM were compared to those derived from electron-density plots based on X-ray crystallographic studies. The conformational features included a bilobal silhouette with an inverted umbrella-shaped crater connected to a reaction site. These studies provide a starting point for constructing a 3D-AFM profiling analysis of proteins such as RNA polymerase complexes

  20. Localization and force analysis at the single virus particle level using atomic force microscopy

    International Nuclear Information System (INIS)

    Liu, Chih-Hao; Horng, Jim-Tong; Chang, Jeng-Shian; Hsieh, Chung-Fan; Tseng, You-Chen; Lin, Shiming

    2012-01-01

    Highlights: ► Localization of single virus particle. ► Force measurements. ► Force mapping. -- Abstract: Atomic force microscopy (AFM) is a vital instrument in nanobiotechnology. In this study, we developed a method that enables AFM to simultaneously measure specific unbinding force and map the viral glycoprotein at the single virus particle level. The average diameter of virus particles from AFM images and the specificity between the viral surface antigen and antibody probe were integrated to design a three-stage method that sets the measuring area to a single virus particle before obtaining the force measurements, where the influenza virus was used as the object of measurements. Based on the purposed method and performed analysis, several findings can be derived from the results. The mean unbinding force of a single virus particle can be quantified, and no significant difference exists in this value among virus particles. Furthermore, the repeatability of the proposed method is demonstrated. The force mapping images reveal that the distributions of surface viral antigens recognized by antibody probe were dispersed on the whole surface of individual virus particles under the proposed method and experimental criteria; meanwhile, the binding probabilities are similar among particles. This approach can be easily applied to most AFM systems without specific components or configurations. These results help understand the force-based analysis at the single virus particle level, and therefore, can reinforce the capability of AFM to investigate a specific type of viral surface protein and its distributions.

  1. Hydrogen atoms in a strong magnetic field

    International Nuclear Information System (INIS)

    Santos, R.R. dos.

    1975-07-01

    The energies and wave functions of the 14 lowest states of a Hydrogen atom in a strong magnetic field are calculated, using a variational scheme. The equivalence between the atomic problem and the problems related with excitons and impurities in semiconductors in the presence of a strong magnetic field are shown. The calculations of the energies and wave functions have been divided in two regions: the first, for the magnetic field ranging between zero and 10 9 G; in the second the magnetic field ranges between 10 9 and 10 11 G. The results have been compared with those obtained by previous authors. The computation time necessary for the calculations is small. Therefore this is a convenient scheme to obtain the energies and wave functions for the problem. Transition probabilities, wavelengths and oscillator strengths for some allowed transitions are also calculated. (Author) [pt

  2. Reconstruction of Undersampled Atomic Force Microscopy Images

    DEFF Research Database (Denmark)

    Jensen, Tobias Lindstrøm; Arildsen, Thomas; Østergaard, Jan

    2013-01-01

    Atomic force microscopy (AFM) is one of the most advanced tools for high-resolution imaging and manipulation of nanoscale matter. Unfortunately, standard AFM imaging requires a timescale on the order of seconds to minutes to acquire an image which makes it complicated to observe dynamic processes....... Moreover, it is often required to take several images before a relevant observation region is identified. In this paper we show how to significantly reduce the image acquisition time by undersampling. The reconstruction of an undersampled AFM image can be viewed as an inpainting, interpolating problem...... should be reconstructed using interpolation....

  3. Cold atoms near superconductors: atomic spin coherence beyond the Johnson noise limit

    International Nuclear Information System (INIS)

    Kasch, B; Hattermann, H; Cano, D; Judd, T E; Zimmermann, C; Kleiner, R; Koelle, D; Fortagh, J; Scheel, S

    2010-01-01

    We report on the measurement of atomic spin coherence near the surface of a superconducting niobium wire. As compared to normal conducting metal surfaces, the atomic spin coherence is maintained for time periods beyond the Johnson noise limit. The result provides experimental evidence that magnetic near-field noise near the superconductor is strongly suppressed. Such long atomic spin coherence times near superconductors open the way towards the development of coherently coupled cold atom/solid state hybrid quantum systems with potential applications in quantum information processing and precision force sensing.

  4. The numerical multiconfiguration self-consistent field approach for atoms; Der numerische Multiconfiguration Self-Consistent Field-Ansatz fuer Atome

    Energy Technology Data Exchange (ETDEWEB)

    Stiehler, Johannes

    1995-12-15

    The dissertation uses the Multiconfiguration Self-Consistent Field Approach to specify the electronic wave function of N electron atoms in a static electrical field. It presents numerical approaches to describe the wave functions and introduces new methods to compute the numerical Fock equations. Based on results computed with an implemented computer program the universal application, flexibility and high numerical precision of the presented approach is shown. RHF results and for the first time MCSCF results for polarizabilities and hyperpolarizabilities of various states of the atoms He to Kr are discussed. In addition, an application to interpret a plasma spectrum of gallium is presented. (orig.)

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

    Science.gov (United States)

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

    2015-08-15

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

  6. The use of atomic force microscopy to evaluate warm mix asphalt.

    Science.gov (United States)

    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...

  7. Finite-field evaluation of the Lennard-Jones atom-wall interaction constant C3 for alkali-metal atoms

    International Nuclear Information System (INIS)

    Johnson, W.R.; Dzuba, V.A.; Safronova, U.I.; Safronova, M.S.

    2004-01-01

    A finite-field scaling method is applied to evaluate the Lennard-Jones interaction constant C 3 for alkali-metal atoms. The calculations are based on the relativistic single-double approximation in which single and double excitations of Dirac-Hartree-Fock wave functions are included to all orders in perturbation theory

  8. Atomic force microscopy applied to study macromolecular content of embedded biological material

    Energy Technology Data Exchange (ETDEWEB)

    Matsko, Nadejda B. [Electron Microscopy Centre, Institute of Applied Physics, HPM C 15.1, ETH-Hoenggerberg, CH-8093, Zurich (Switzerland)]. E-mail: matsko@iap.phys.ethz.ch

    2007-02-15

    We demonstrate that atomic force microscopy represents a powerful tool for the estimation of structural preservation of biological samples embedded in epoxy resin, in terms of their macromolecular distribution and architecture. The comparison of atomic force microscopy (AFM) and transmission electron microscopy (TEM) images of a biosample (Caenorhabditis elegans) prepared following to different types of freeze-substitution protocols (conventional OsO{sub 4} fixation, epoxy fixation) led to the conclusion that high TEM stainability of the sample results from a low macromolecular density of the cellular matrix. We propose a novel procedure aimed to obtain AFM and TEM images of the same particular organelle, which strongly facilitates AFM image interpretation and reveals new ultrastructural aspects (mainly protein arrangement) of a biosample in addition to TEM data.

  9. Origins of phase contrast in the atomic force microscope in liquids

    OpenAIRE

    Melcher, John; Carrasco, Carolina; Xu, Xianfan; Carrascosa, Jose L; Gomez-Herrero, Julio; Jose de Pablo, Pedro; Raman, Arvind

    2009-01-01

    We study the physical origins of phase contrast in dynamic atomic force microscopy (dAFM) in liquids where low-stiffness microcantilever probes are often used for nanoscale imaging of soft biological samples with gentle forces. Under these conditions, we show that the phase contrast derives primarily from a unique energy flow channel that opens up in liquids due to the momentary excitation of higher eigenmodes. Contrary to the common assumption, phase-contrast images in liquids using soft mic...

  10. Transversal light forces in semiconductors

    CERN Document Server

    Lindberg, M

    2003-01-01

    The transversal light force is a well established effect in atomic and molecular systems that are exposed to spatially inhomogeneous light fields. In this paper it is shown theoretically that in an excited semiconductor, containing an electron-hole plasma or excitons, a similar light force exists, if the semiconductor is exposed to an ultrashort spatially inhomogeneous light field. The analysis is based on the equations of motion for the Wigner distribution functions of charge carrier populations and interband polarizations. The results show that, while the light force on the electron-hole plasma or the excitons does exist, its effects on the kinetic behaviour of the electron-hole plasma or the excitons are different compared to the situation in an atomic or molecular system. A detailed analysis presented here traces this difference back to the principal differences between atoms and molecules on the one hand and electron-hole plasmas or excitons on the other hand.

  11. A subsurface add-on for standard atomic force microscopes

    Energy Technology Data Exchange (ETDEWEB)

    Verbiest, G. J., E-mail: Verbiest@physik.rwth-aachen.de [JARA-FIT and II. Institute of Physics, RWTH Aachen University, 52074 Aachen (Germany); Zalm, D. J. van der; Oosterkamp, T. H.; Rost, M. J., E-mail: Rost@physics.leidenuniv.nl [Kamerlingh Onnes Laboratory, Leiden University, P.O. Box 9504, 2300 RA Leiden (Netherlands)

    2015-03-15

    The application of ultrasound in an Atomic Force Microscope (AFM) gives access to subsurface information. However, no commercially AFM exists that is equipped with this technique. The main problems are the electronic crosstalk in the AFM setup and the insufficiently strong excitation of the cantilever at ultrasonic (MHz) frequencies. In this paper, we describe the development of an add-on that provides a solution to these problems by using a special piezo element with a lowest resonance frequency of 2.5 MHz and by separating the electronic connection for this high frequency piezo element from all other connections. In this sense, we support researches with the possibility to perform subsurface measurements with their existing AFMs and hopefully pave also the way for the development of a commercial AFM that is capable of imaging subsurface features with nanometer resolution.

  12. Structure of ordered polyelectrolyte films from atomic-force microscopy and X-ray reflectivity data

    International Nuclear Information System (INIS)

    Belyaev, V.V.; Tolstikhina, A.L.; Stepina, N.D.; Kayushina, R.L.

    1998-01-01

    The possible application of atomic-force microscopy and X-ray reflectometry methods to structural studies of polyelectrolyte films obtained due to alternating adsorption of oppositely charged polyanion [sodium polysterenesulfonate (PSS)] and polycation [poly(allylamine) hydrochloride (PAA)] layers on solid substrates has been considered. The atomic-force microscopy study has revealed the characteristic features of the surface topography of samples consisting of different numbers of polyelectrolyte layers deposited from solutions characterized by different ionic strength values. It is shown that the shape of the reflectivity curves obtained from thin polyelectrolyte films depends on their surface structure

  13. Origin of current-induced forces in an atomic gold wire: A first-principles study

    DEFF Research Database (Denmark)

    Brandbyge, Mads; Stokbro, Kurt; Taylor, Jeremy Philip

    2003-01-01

    We address the microscopic origin of the current-induced forces by analyzing results of first principles density functional calculations of atomic gold wires connected to two gold electrodes with different electrochemical potentials. We find that current induced forces are closely related...

  14. A new ion sensing deep atomic force microscope

    Energy Technology Data Exchange (ETDEWEB)

    Drake, Barney; Randall, Connor; Bridges, Daniel; Hansma, Paul K. [Department of Physics, University of California, Santa Barbara, California 93106 (United States)

    2014-08-15

    Here we describe a new deep atomic force microscope (AFM) capable of ion sensing. A novel probe assembly incorporates a micropipette that can be used both for sensing ion currents and as the tip for AFM imaging. The key advance of this instrument over previous ion sensing AFMs is that it uses conventional micropipettes in a novel suspension system. This paper focuses on sensing the ion current passively while using force feedback for the operation of the AFM in contact mode. Two images are obtained simultaneously: (1) an AFM topography image and (2) an ion current image. As an example, two images of a MEMS device with a microchannel show peaks in the ion current as the pipette tip goes over the edges of the channel. This ion sensing AFM can also be used in other modes including tapping mode with force feedback as well as in non-contact mode by utilizing the ion current for feedback, as in scanning ion conductance microscopy. The instrument is gentle enough to be used on some biological samples such as plant leaves.

  15. Investigating single molecule adhesion by atomic force spectroscopy.

    Science.gov (United States)

    Stetter, Frank W S; Kienle, Sandra; Krysiak, Stefanie; Hugel, Thorsten

    2015-02-27

    Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment.

  16. A new image correction method for live cell atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Y; Sun, J L; Zhang, A; Hu, J; Xu, L X [College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030 (China)

    2007-04-21

    During live cell imaging via atomic force microscopy (AFM), the interactions between the AFM probe and the membrane yield distorted cell images. In this work, an image correction method was developed based on the force-distance curve and the modified Hertzian model. The normal loading and lateral forces exerted on the cell membrane by the AFM tip were both accounted for during the scanning. Two assumptions were made in modelling based on the experimental measurements: (1) the lateral force on the endothelial cells was linear to the height; (2) the cell membrane Young's modulus could be derived from the displacement measurement of a normal force curve. Results have shown that the model could be used to recover up to 30% of the actual cell height depending on the loading force. The accuracy of the model was also investigated with respect to the loading force and mechanical property of the cell membrane.

  17. Dynamics of atom-field entanglement for Tavis-Cummings models

    Science.gov (United States)

    Bashkirov, Eugene K.

    2018-04-01

    An exact solution of the problem of two-atom one- and two-mode Jaynes-Cummings model with intensity- dependent coupling is presented. Asymptotic solutions for system state vectors are obtained in the approximation of large initial coherent fields. The atom-field entanglement is investigated on the basis of the reduced atomic entropy dynamics. The possibility of the system being initially in a pure disentangled state to revive into this state during the evolution process for both models is shown. Conditions and times of disentanglement are derived.

  18. Microfluidic Platform for the Elastic Characterization of Mouse Submandibular Glands by Atomic Force Microscopy

    Directory of Open Access Journals (Sweden)

    Aaron P. Mosier

    2014-02-01

    Full Text Available The ability to characterize the microscale mechanical properties of biological materials has the potential for great utility in the field of tissue engineering. The development and morphogenesis of mammalian tissues are known to be guided in part by mechanical stimuli received from the local environment, and tissues frequently develop to match the physical characteristics (i.e., elasticity of their environment. Quantification of these material properties at the microscale may provide valuable information to guide researchers. Presented here is a microfluidic platform for the non-destructive ex vivo microscale mechanical characterization of mammalian tissue samples by atomic force microscopy (AFM. The device was designed to physically hold a tissue sample in a dynamically controllable fluid environment while allowing access by an AFM probe operating in force spectroscopy mode to perform mechanical testing. Results of measurements performed on mouse submandibular gland samples demonstrate the ability of the analysis platform to quantify sample elasticity at the microscale, and observe chemically-induced changes in elasticity.

  19. Influence of the virtual photon field on the squeezing properties of an atom laser

    International Nuclear Information System (INIS)

    Jian-Gang, Zhao; Chang-Yong, Sun; Ling-Hua, Wen; Bao-Long, Liang

    2009-01-01

    This paper investigates the squeezing properties of an atom laser without rotating-wave approximation in the system of a binomial states field interacting with a two-level atomic Bose–Einstein condensate. It discusses the influences of atomic eigenfrequency, the interaction intensity between the optical field and atoms, parameter of the binomial states field and virtual photon field on the squeezing properties. The results show that two quadrature components of an atom laser can be squeezed periodically. The duration and the degree of squeezing an atom laser have something to do with the atomic eigenfrequency and the parameter of the binomial states field, respectively. The collapse and revival frequency of atom laser fluctuation depends on the interaction intensity between the optical field and atoms. The effect of the virtual photon field deepens the depth of squeezing an atom laser

  20. Nanoscans of piezoelectric activity using an atomic force microscope

    International Nuclear Information System (INIS)

    Zheng, Z.; Guy, I.L.; Butcher, K.S.A.; Tansley, T.L.

    2002-01-01

    Full text: Any crystal which lacks a centre of symmetry is piezoelectric. This includes all of the ferroelectric crystals used in photonics and virtually all compound semiconductors. Such crystals, when grown in thin film form invariably exist in a strained state and thus possess internal piezoelectric fields which can affect their electronic properties. A knowledge of the piezoelectric properties of such crystals is thus important in understanding how they behave in practical devices. It also provides a tool for analysing the crystal structure of such materials. Using an atomic force microscope (AFM) as a probe of piezoelectric activity allows the study of variations in crystal structure on a nanoscale. The AFM piezoelectric technique has been used by several groups to study structures of ceramic materials with large piezoelectric coefficients, intended for applications in piezoelectric actuators. In the AFM method, a driving signal of a few volts at a frequency well below the AFM tip resonance, is applied to a sample of the material mounted in the AFM. This voltage causes the sample dimensions to change in ways determined by the piezoelectric properties of the sample. The AFM signal thus contains the normal surface profile information and an additional component generated by the piezoelectric vibrations of the sample. A lockin amplifier is used to separate the piezoelectric signal from the normal AFM surface profile signal. The result is the simultaneous acquisition of the surface profile and a piezoelectric map of the surface of the material under study. We will present results showing the results of such measurements in materials such as lithium niobate and gallium nitride. These materials have piezoelectric coefficients which are much lower than those of materials to which the technique has normally been applied

  1. Nuclear Forces from Effective Field Theory

    International Nuclear Information System (INIS)

    Krebs, H.

    2011-01-01

    Chiral effective field theory allows for a systematic and model-independent derivation of the forces between nucleons in harmony with the symmetries of the quantum chromodynamics. After a brief review on the current status in the development of the chiral nuclear forces I will focus on the role of the Δ-resonance contributions in the nuclear dynamics.We find improvement in the convergence of the chiral expansion of the nuclear forces if we explicitly take into account the Δ-resonance degrees of freedom. The overall results for two-nucleon forces with and without explicit Δ-resonance degrees of freedom are remarkably similar. We discussed the long- and shorter-range N 3 LO contributions to chiral three-nucleon forces. No additional free parameters appear at this order. There are five different topology classes which contribute to the forces. Three of them describe long-range contributions which constitute the first systematic corrections to the leading 2π exchange that appear at N 2 LO. Another two contributions are of a shorter range and include, additionally to an exchange of pions, also one short-range contact interaction and all corresponding 1/m corrections. The requirement of renormalizability leads to unique expressions for N 3 LO contributions to the three-nucleon force (except for 1/m-corrections). We presented the complete N 2 LO analysis of the nuclear forces with explicit Δ-isobar degrees of freedom. Although the overall results in the isospin-conserving case are very similar in the Δ-less and Δ-full theories, we found a much better convergence in all peripheral partial waves once Δ-resonance is explicitly taken into account. The leading CSB contributions to nuclear forces are proportional to nucleon- and Δ-mass splittings. There appear strong cancellations between the two contributions which at leading order yield weaker V III potentials. This effect is, however, entirely compensated at subleading order such that the results in the theories

  2. Probing dark energy with atom interferometry

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  3. Probing dark energy with atom interferometry

    Energy Technology Data Exchange (ETDEWEB)

    Burrage, Clare; Copeland, Edmund J. [School of Physics and Astronomy, University of Nottingham, Nottingham, NG7 2RD (United Kingdom); Hinds, E.A., E-mail: Clare.Burrage@nottingham.ac.uk, E-mail: Edmund.Copeland@nottingham.ac.uk, E-mail: Ed.Hinds@imperial.ac.uk [Centre for Cold Matter, Blackett Laboratory, Imperial College London, Prince Consort Road, London, SW7 2AZ (United Kingdom)

    2015-03-01

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

  4. Langmuir- Blodgett layers of amphiphilic molecules investigated by Atomic Force Microscopy

    NARCIS (Netherlands)

    Zdravkova, Aneliya Nikolova

    2007-01-01

    Langmuir - Blodgett technique and Atomic Force Microscopy were used to study the phase behaviour of organic molecules (fatty alcohols and monoacid saturated triglycerides) at air-water and air-solid interfaces. The structure of binary mixed LB monolayers of fatty alcohols was reported. The

  5. Theoretical atomic-force-microscopy study of a stepped surface: Nonlocal effects in the probe

    International Nuclear Information System (INIS)

    Girard, C.

    1991-01-01

    The interaction force between a metallic tip and a nonplanar dielectric surface is derived from a nonlocal formalism. A general formulation is given for the case of a spherical tip of nanometer size and for surfaces of arbitrary shapes (stepped surfaces and single crystals adsorbed on a planar surface). The dispersion part of the attractive force is obtained from a nonlocal theory expressed in terms of generalized electric susceptibilities of the two constituents. Implications for atomic force microscopy in attractive modes are discussed. In this context, the present model indicates two different forms of corrugation: those due to the protuberance present on the tip leading to atomic corrugations; nanometer-sized corrugations detected in the attractive region by the spherical part of the tip

  6. A Computer-Controlled Classroom Model of an Atomic Force Microscope

    Science.gov (United States)

    Engstrom, Tyler A.; Johnson, Matthew M.; Eklund, Peter C.; Russin, Timothy J.

    2015-01-01

    The concept of "seeing by feeling" as a way to circumvent limitations on sight is universal on the macroscopic scale--reading Braille, feeling one's way around a dark room, etc. The development of the atomic force microscope (AFM) in 1986 extended this concept to imaging in the nanoscale. While there are classroom demonstrations that use…

  7. Laser sub-Doppler cooling of atoms in an arbitrarily directed magnetic field

    International Nuclear Information System (INIS)

    Chang, Soo; Kwon, Taeg Yong; Lee, Ho Seong; Minogin, V.G.

    2002-01-01

    We analyze the influence of an arbitrarily directed uniform magnetic field on the laser sub-Doppler cooling of atoms. The analysis is done for a (3+5)-level atom excited by a σ + -σ - laser field configuration. Our analysis shows that the effects of the magnetic field depend strongly on the direction of the magnetic field. In an arbitrarily directed magnetic field the laser cooling configuration produces both the main resonance existing already at zero magnetic field and additional sub-Doppler resonances caused by two-photon and higher-order multiphoton processes. These sub-Doppler resonances are, however, well separated on the velocity scale if the Zeeman shift exceeds the widths of the resonances. This allows one to use the main sub-Doppler resonance for an effective laser cooling of atoms even in the presence of the magnetic field. The effective temperature of the atomic ensemble at the velocity of the main resonance is found to be almost the same as in the absence of the magnetic field. The defined structure of the multiphoton resonances may be of importance for the sub-Doppler laser cooling of atoms, atomic extraction from magneto-optical traps, and applications related to the control of atomic motion

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

    Science.gov (United States)

    Leib, Raz; Karniel, Amir; Nisky, Ilana

    2015-05-01

    During interaction with objects, we form an internal representation of their mechanical properties. This representation is used for perception and for guiding actions, such as in precision grip, where grip force is modulated with the predicted load forces. In this study, we explored the relationship between grip force adjustment and perception of stiffness during interaction with linear elastic force fields. In a forced-choice paradigm, participants probed pairs of virtual force fields while grasping a force sensor that was attached to a haptic device. For each pair, they were asked which field had higher level of stiffness. In half of the pairs, the force feedback of one of the fields was delayed. Participants underestimated the stiffness of the delayed field relatively to the nondelayed, but their grip force characteristics were similar in both conditions. We analyzed the magnitude of the grip force and the lag between the grip force and the load force in the exploratory probing movements within each trial. Right before answering which force field had higher level of stiffness, both magnitude and lag were similar between delayed and nondelayed force fields. These results suggest that an accurate internal representation of environment stiffness and time delay was used for adjusting the grip force. However, this representation did not help in eliminating the bias in stiffness perception. We argue that during performance of a perceptual task that is based on proprioceptive feedback, separate neural mechanisms are responsible for perception and action-related computations in the brain. Copyright © 2015 the American Physiological Society.

  9. Localization and force analysis at the single virus particle level using atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Chih-Hao [Institute of Applied Mechanics, Nation Taiwan University, Roosevelt Road, Taipei 10617, Taiwan (China); Horng, Jim-Tong [Department of Biochemistry, Chang Gung University, 259 Wen-Hwa First Road, Kweishan, Taoyuan 333, Taiwan (China); Chang, Jeng-Shian [Institute of Applied Mechanics, Nation Taiwan University, Roosevelt Road, Taipei 10617, Taiwan (China); Hsieh, Chung-Fan [Graduate Institute of Biomedical Sciences, Chang Gung University, Kweishan, Taoyuan 333, Taiwan (China); Tseng, You-Chen [Institute of Applied Mechanics, Nation Taiwan University, Roosevelt Road, Taipei 10617, Taiwan (China); Lin, Shiming, E-mail: til@ntu.edu.tw [Institute of Applied Mechanics, Nation Taiwan University, Roosevelt Road, Taipei 10617, Taiwan (China); Center for Optoelectronic Biomedicine, College of Medicine, Nation Taiwan University, 1-1 Jen-Ai Road, Taipei 10051, Taiwan (China)

    2012-01-06

    Highlights: Black-Right-Pointing-Pointer Localization of single virus particle. Black-Right-Pointing-Pointer Force measurements. Black-Right-Pointing-Pointer Force mapping. -- Abstract: Atomic force microscopy (AFM) is a vital instrument in nanobiotechnology. In this study, we developed a method that enables AFM to simultaneously measure specific unbinding force and map the viral glycoprotein at the single virus particle level. The average diameter of virus particles from AFM images and the specificity between the viral surface antigen and antibody probe were integrated to design a three-stage method that sets the measuring area to a single virus particle before obtaining the force measurements, where the influenza virus was used as the object of measurements. Based on the purposed method and performed analysis, several findings can be derived from the results. The mean unbinding force of a single virus particle can be quantified, and no significant difference exists in this value among virus particles. Furthermore, the repeatability of the proposed method is demonstrated. The force mapping images reveal that the distributions of surface viral antigens recognized by antibody probe were dispersed on the whole surface of individual virus particles under the proposed method and experimental criteria; meanwhile, the binding probabilities are similar among particles. This approach can be easily applied to most AFM systems without specific components or configurations. These results help understand the force-based analysis at the single virus particle level, and therefore, can reinforce the capability of AFM to investigate a specific type of viral surface protein and its distributions.

  10. A hybrid polarization-selective atomic sensor for radio-frequency field detection with a passive resonant-cavity field amplifier

    OpenAIRE

    Anderson, David A.; Paradis, Eric G.; Raithel, Georg

    2018-01-01

    We present a hybrid atomic sensor that realizes radio-frequency electric field detection with intrinsic field amplification and polarization selectivity for robust high-sensitivity field measurement. The hybrid sensor incorporates a passive resonator element integrated with an atomic vapor cell that provides amplification and polarization selectivity for detection of incident radio-frequency fields. The amplified intra-cavity radio-frequency field is measured by atoms using a quantum-optical ...

  11. [Atomic force microscopy: a tool to analyze the viral cycle].

    Science.gov (United States)

    Bernaud, Julien; Castelnovo, Martin; Muriaux, Delphine; Faivre-Moskalenko, Cendrine

    2015-05-01

    Each step of the HIV-1 life cycle frequently involves a change in the morphology and/or mechanical properties of the viral particle or core. The atomic force microscope (AFM) constitutes a powerful tool for characterizing these physical changes at the scale of a single virus. Indeed, AFM enables the visualization of viral capsids in a controlled physiological environment and to probe their mechanical properties by nano-indentation. Finally, AFM force spectroscopy allows to characterize the affinities between viral envelope proteins and cell receptors at the single molecule level. © 2015 médecine/sciences – Inserm.

  12. Quantum optics. All-optical routing of single photons by a one-atom switch controlled by a single photon.

    Science.gov (United States)

    Shomroni, Itay; Rosenblum, Serge; Lovsky, Yulia; Bechler, Orel; Guendelman, Gabriel; Dayan, Barak

    2014-08-22

    The prospect of quantum networks, in which quantum information is carried by single photons in photonic circuits, has long been the driving force behind the effort to achieve all-optical routing of single photons. We realized a single-photon-activated switch capable of routing a photon from any of its two inputs to any of its two outputs. Our device is based on a single atom coupled to a fiber-coupled, chip-based microresonator. A single reflected control photon toggles the switch from high reflection (R ~ 65%) to high transmission (T ~ 90%), with an average of ~1.5 control photons per switching event (~3, including linear losses). No additional control fields are required. The control and target photons are both in-fiber and practically identical, making this scheme compatible with scalable architectures for quantum information processing. Copyright © 2014, American Association for the Advancement of Science.

  13. Atomic Force Microscopy - A Tool to Unveil the Mystery of Biological ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 7. Atomic Force Microscopy - A Tool to Unveil the Mystery of Biological Systems ... Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560 ...

  14. Atomic insight into tribochemical wear mechanism of silicon at the Si/SiO{sub 2} interface in aqueous environment: Molecular dynamics simulations using ReaxFF reactive force field

    Energy Technology Data Exchange (ETDEWEB)

    Wen, Jialin; Ma, Tianbao [State Key Laboratory of Tribology, Tsinghua University, Beijing 100084 (China); Zhang, Weiwei; Psofogiannakis, George; Duin, Adri C.T. van [Department of Mechanical and Nuclear Engineering, Pennsylvania State University, University Park, PA 16802 (United States); Chen, Lei; Qian, Linmao [Tribology Research Institute, Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031 (China); Hu, Yuanzhong [State Key Laboratory of Tribology, Tsinghua University, Beijing 100084 (China); Lu, Xinchun, E-mail: xclu@tsinghua.edu.cn [State Key Laboratory of Tribology, Tsinghua University, Beijing 100084 (China)

    2016-12-30

    Highlights: • New ReaxFF reactive force field was applied to simulate the tribochemical wear process at Si/SiO{sub 2} interface. • Wear of silicon atoms is due to the breaking of Si–O–Si bonds and Si–Si–O–Si bond chains on the Si substrate. • Interfacial bridge bonds play an important role during the tribochemical wear process. • Higher pressures applied to the silica phase can cause more Si atoms to be removed by forming more interfacial bridge bonds. • Water plays an opposing role in the wear process because of its both chemical and mechanical effects. - Abstract: In this work, the atomic mechanism of tribochemical wear of silicon at the Si/SiO{sub 2} interface in aqueous environment was investigated using ReaxFF molecular dynamics (MD) simulations. Two types of Si atom removal pathways were detected in the wear process. The first is caused by the destruction of stretched Si–O–Si bonds on the Si substrate surface and is assisted by the attachment of H atoms on the bridging oxygen atoms of the bonds. The other is caused by the rupture of Si–Si bonds in the stretched Si–Si–O–Si bond chains at the interface. Both pathways effectively remove Si atoms from the silicon surface via interfacial Si–O–Si bridge bonds. Our simulations also demonstrate that higher pressures applied to the silica phase can cause more Si atoms to be removed due to the formation of increased numbers of interfacial Si–O–Si bridge bonds. Besides, water plays a dual role in the wear mechanism, by oxidizing the Si substrate surface as well as by preventing the close contact of the surfaces. This work shows that the removal of Si atoms from the substrate is a result of both chemical reaction and mechanical effects and contributes to the understanding of tribochemical wear behavior in the microelectromechanical systems (MEMS) and Si chemical mechanical polishing (CMP) process.

  15. Detection of magnetic-labeled antibody specific recognition events by combined atomic force and magnetic force microscopy

    International Nuclear Information System (INIS)

    Hong Xia; Liu Yanmei; Li Jun; Guo Wei; Bai Yubai

    2009-01-01

    Atomic force (AFM) and magnetic force microscopy (MFM) were developed to detect biomolecular specific interaction. Goat anti-mouse immunoglobulin (anti-IgG) was covalently attached onto gold substrate modified by a self-assembly monolayer of thioctic acid via 1-ethyl-3-[3-(dimethylamino) propyl] carbodiimide (EDC) activation. Magnetic-labeled IgG then specifically adsorbed onto anti-IgG surface. The morphological variation was identified by AFM. MFM was proved to be a fine assistant tool to distinguish the immunorecognized nanocomposites from the impurities by detection of the magnetic signal from magnetic-labeled IgG. It would enhance the understanding of biomolecular recognition process.

  16. Detection of magnetic-labeled antibody specific recognition events by combined atomic force and magnetic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Hong Xia [Center for Advanced Optoelectronic Functional Materials Research, Key Laboratory of UV Light-Emitting Materials and Technology, Ministry of Education, Northeast Normal University, Changchun 130024 (China); College of Chemistry, Jilin University, Changchun 130023 (China)], E-mail: xiahong@nenu.edu.cn; Liu Yanmei; Li Jun; Guo Wei; Bai Yubai [College of Chemistry, Jilin University, Changchun 130023 (China)

    2009-09-15

    Atomic force (AFM) and magnetic force microscopy (MFM) were developed to detect biomolecular specific interaction. Goat anti-mouse immunoglobulin (anti-IgG) was covalently attached onto gold substrate modified by a self-assembly monolayer of thioctic acid via 1-ethyl-3-[3-(dimethylamino) propyl] carbodiimide (EDC) activation. Magnetic-labeled IgG then specifically adsorbed onto anti-IgG surface. The morphological variation was identified by AFM. MFM was proved to be a fine assistant tool to distinguish the immunorecognized nanocomposites from the impurities by detection of the magnetic signal from magnetic-labeled IgG. It would enhance the understanding of biomolecular recognition process.

  17. Higher order structure of short immunostimulatory oligonucleotides studied by atomic force microscopy

    International Nuclear Information System (INIS)

    Klein, Dionne C.G.; Latz, Eicke; Espevik, Terje; Stokke, Bjorn T.

    2010-01-01

    Immunostimulatory CpG-DNA activates the innate immune system by binding to Toll-like receptor 9. Structurally different CpG-containing oligonucleotides trigger a different type of immune response while activating the same receptor. We therefore investigated the higher order structure of two different classes of immunostimulatory CpG-DNA. Class A, which contains a partly self-complementary sequence and poly-G ends, forms duplexes and nanoparticles in salt solution, while class B, which does not contain these features and is purely linear, does not form a duplex or nanoparticles. Results obtained here by high-resolution atomic force microscopy of classes A and B CpG-DNA, reflect these differences in secondary structure. Detailed structural analysis of the atomic force microscopy topographs is presented for two different sample preparation methods.

  18. Higher order structure of short immunostimulatory oligonucleotides studied by atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Klein, Dionne C.G., E-mail: dionne.c.g.klein@ntnu.no [Department of Physics, Norwegian University of Science and Technology, N-7491, Trondheim (Norway); Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Latz, Eicke [Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605 (United States); Institute of Innate Immunity, University Hospitals, University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn (Germany); Espevik, Terje [Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Stokke, Bjorn T. [Department of Physics, Norwegian University of Science and Technology, N-7491, Trondheim (Norway)

    2010-05-15

    Immunostimulatory CpG-DNA activates the innate immune system by binding to Toll-like receptor 9. Structurally different CpG-containing oligonucleotides trigger a different type of immune response while activating the same receptor. We therefore investigated the higher order structure of two different classes of immunostimulatory CpG-DNA. Class A, which contains a partly self-complementary sequence and poly-G ends, forms duplexes and nanoparticles in salt solution, while class B, which does not contain these features and is purely linear, does not form a duplex or nanoparticles. Results obtained here by high-resolution atomic force microscopy of classes A and B CpG-DNA, reflect these differences in secondary structure. Detailed structural analysis of the atomic force microscopy topographs is presented for two different sample preparation methods.

  19. Fluctuation-induced forces on an atom near a photonic topological material

    Science.gov (United States)

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

    2018-02-01

    We theoretically study the Casimir-Polder force on an atom in an arbitrary initial state in a rather general electromagnetic environment wherein the materials may have a nonreciprocal bianisotropic dispersive response. It is shown that under the Markov approximation the force has resonant and nonresonant contributions. We obtain explicit expressions for the optical force both in terms of the system Green function and of the electromagnetic modes. We apply the theory to the particular case wherein a two-level system interacts with a topological gyrotropic material, showing that the nonreciprocity enables exotic light-matter interactions and the opportunity to sculpt and tune the Casimir-Polder forces on the nanoscale. With a quasistatic approximation, we obtain a simple analytical expression for the optical force and unveil the crucial role of surface plasmons in fluctuation-induced forces. Finally, we derive the Green function for a gyrotropic material half-space in terms of a Sommerfeld integral.

  20. Two-dimensional atom localization based on coherent field controlling in a five-level M-type atomic system.

    Science.gov (United States)

    Jiang, Xiangqian; Li, Jinjiang; Sun, Xiudong

    2017-12-11

    We study two-dimensional sub-wavelength atom localization based on the microwave coupling field controlling and spontaneously generated coherence (SGC) effect. For a five-level M-type atom, introducing a microwave coupling field between two upper levels and considering the quantum interference between two transitions from two upper levels to lower levels, the analytical expression of conditional position probability (CPP) distribution is obtained using the iterative method. The influence of the detuning of a spontaneously emitted photon, Rabi frequency of the microwave field, and the SGC effect on the CPP are discussed. The two-dimensional sub-half-wavelength atom localization with high-precision and high spatial resolution is achieved by adjusting the detuning and the Rabi frequency, where the atom can be localized in a region smaller thanλ/10×λ/10. The spatial resolution is improved significantly compared with the case without the microwave field.

  1. Measurement of the force on microparticles in a beam of energetic ions and neutral atoms

    International Nuclear Information System (INIS)

    Trottenberg, Thomas; Schneider, Viktor; Kersten, Holger

    2010-01-01

    The force on microparticles in an energetic ion beam is investigated experimentally. Hollow glass microspheres are injected into the vertically upward directed beam and their trajectories are recorded with a charge-coupled device camera. The net force on the particles is determined by means of the measured vertical acceleration. The resulting beam pressures are compared with Faraday cup measurements of the ion current density and calorimetric measurements of the beam power density. Due to the neutral gas background, the beam consists, besides the ions, of energetic neutral atoms produced by charge-exchange collisions. It is found that the measured composition of the drag force by an ion and a neutral atom component agrees with a beam model that takes charge-exchange collisions into account. Special attention is paid to the momentum contribution from sputtered atoms, which is shown to be negligible in this experiment, but should become measurable in case of materials with high sputtering yields.

  2. Tip radius preservation for high resolution imaging in amplitude modulation atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ramos, Jorge R., E-mail: jorge.rr@cea.cu [Instituto de Ciencia de Materiales de Madrid, Sor Juana Inés de la Cruz 3, Canto Blanco, 28049 Madrid, España (Spain)

    2014-07-28

    The acquisition of high resolution images in atomic force microscopy (AFM) is correlated to the cantilever's tip shape, size, and imaging conditions. In this work, relative tip wear is quantified based on the evolution of a direct experimental observable in amplitude modulation atomic force microscopy, i.e., the critical amplitude. We further show that the scanning parameters required to guarantee a maximum compressive stress that is lower than the yield/fracture stress of the tip can be estimated via experimental observables. In both counts, the optimized parameters to acquire AFM images while preserving the tip are discussed. The results are validated experimentally by employing IgG antibodies as a model system.

  3. Explicit all-atom modeling of realistically sized ligand-capped nanocrystals

    KAUST Repository

    Kaushik, Ananth P.; Clancy, Paulette

    2012-01-01

    We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), capped with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well

  4. High-speed atomic force microscopy coming of age

    International Nuclear Information System (INIS)

    Ando, Toshio

    2012-01-01

    High-speed atomic force microscopy (HS-AFM) is now materialized. It allows direct visualization of dynamic structural changes and dynamic processes of functioning biological molecules in physiological solutions, at high spatiotemporal resolution. Dynamic molecular events unselectively appear in detail in an AFM movie, facilitating our understanding of how biological molecules operate to function. This review describes a historical overview of technical development towards HS-AFM, summarizes elementary devices and techniques used in the current HS-AFM, and then highlights recent imaging studies. Finally, future challenges of HS-AFM studies are briefly discussed. (topical review)

  5. High-speed atomic force microscopy coming of age

    Science.gov (United States)

    Ando, Toshio

    2012-02-01

    High-speed atomic force microscopy (HS-AFM) is now materialized. It allows direct visualization of dynamic structural changes and dynamic processes of functioning biological molecules in physiological solutions, at high spatiotemporal resolution. Dynamic molecular events unselectively appear in detail in an AFM movie, facilitating our understanding of how biological molecules operate to function. This review describes a historical overview of technical development towards HS-AFM, summarizes elementary devices and techniques used in the current HS-AFM, and then highlights recent imaging studies. Finally, future challenges of HS-AFM studies are briefly discussed.

  6. Force on an electric/magnetic dipole and classical approach to spin-orbit coupling in hydrogen-like atoms

    Science.gov (United States)

    Kholmetskii, A. L.; Missevitch, O. V.; Yarman, T.

    2017-09-01

    We carry out the classical analysis of spin-orbit coupling in hydrogen-like atoms, using the modern expressions for the force and energy of an electric/magnetic dipole in an electromagnetic field. We disclose a novel physical meaning of this effect and show that for a laboratory observer the energy of spin-orbit interaction is represented solely by the mechanical energy of the spinning electron (considered as a gyroscope) due to the Thomas precession of its spin. Concurrently we disclose some errors in the old and new publications on this subject.

  7. Shear force distance control in a scanning near-field optical microscope: in resonance excitation of the fiber probe versus out of resonance excitation

    International Nuclear Information System (INIS)

    Lapshin, D.A.; Letokhov, V.S.; Shubeita, G.T.; Sekatskii, S.K.; Dietler, G.

    2004-01-01

    The experimental results of the direct measurement of the absolute value of interaction force between the fiber probe of a scanning near-field optical microscope (SNOM) operated in shear force mode and a sample, which were performed using combined SNOM-atomic force microscope setup, are discussed for the out-of-resonance fiber probe excitation mode. We demonstrate that the value of the tapping component of the total force for this mode at typical dither amplitudes is of the order of 10 nN and thus is quite comparable with the value of this force for in resonance fiber probe excitation mode. It is also shown that for all modes this force component is essentially smaller than the usually neglected static attraction force, which is of the order of 200 nN. The true contact nature of the tip-sample interaction during the out of resonance mode is proven. From this, we conclude that such a detection mode is very promising for operation in liquids, where other modes encounter great difficulties

  8. Chaotic scattering from hydrogen atoms in a circularly polarized laser field

    International Nuclear Information System (INIS)

    Okon, Elias; Parker, William; Chism, Will; Reichl, Linda E.

    2002-01-01

    We investigate the classical dynamics of a hydrogen atom in a circularly polarized laser beam with finite radius. The spatial cutoff for the laser field allows us to use scattering processes to examine the laser-atom dynamics. We find that for certain field parameters, the delay times, the angular momentum, and the distance of closest approach of the scattered electron exhibit fractal behavior. This fractal behavior is a signature of chaos in the dynamics of the atom-field system

  9. Nanostructure and force spectroscopy analysis of human peripheral blood CD4+ T cells using atomic force microscopy

    International Nuclear Information System (INIS)

    Hu Mingqian; Wang Jiongkun; Cai Jiye; Wu Yangzhe; Wang Xiaoping

    2008-01-01

    To date, nanoscale imaging of the morphological changes and adhesion force of CD4 + T cells during in vitro activation remains largely unreported. In this study, we used atomic force microscopy (AFM) to study the morphological changes and specific binding forces in resting and activated human peripheral blood CD4 + T cells. The AFM images revealed that the volume of activated CD4 + T cells increased and the ultrastructure of these cells also became complex. Using a functionalized AFM tip, the strength of the specific binding force of the CD4 antigen-antibody interaction was found to be approximately three times that of the unspecific force. The adhesion forces were not randomly distributed over the surface of a single activated CD4 + T cell, indicated that the CD4 molecules concentrated into nanodomains. The magnitude of the adhesion force of the CD4 antigen-antibody interaction did not change markedly with the activation time. Multiple bonds involved in the CD4 antigen-antibody interaction were measured at different activation times. These results suggest that the adhesion force involved in the CD4 antigen-antibody interaction is highly selective and of high affinity

  10. Nanostructure and force spectroscopy analysis of human peripheral blood CD4+ T cells using atomic force microscopy.

    Science.gov (United States)

    Hu, Mingqian; Wang, Jiongkun; Cai, Jiye; Wu, Yangzhe; Wang, Xiaoping

    2008-09-12

    To date, nanoscale imaging of the morphological changes and adhesion force of CD4(+) T cells during in vitro activation remains largely unreported. In this study, we used atomic force microscopy (AFM) to study the morphological changes and specific binding forces in resting and activated human peripheral blood CD4(+) T cells. The AFM images revealed that the volume of activated CD4(+) T cells increased and the ultrastructure of these cells also became complex. Using a functionalized AFM tip, the strength of the specific binding force of the CD4 antigen-antibody interaction was found to be approximately three times that of the unspecific force. The adhesion forces were not randomly distributed over the surface of a single activated CD4(+) T cell, indicated that the CD4 molecules concentrated into nanodomains. The magnitude of the adhesion force of the CD4 antigen-antibody interaction did not change markedly with the activation time. Multiple bonds involved in the CD4 antigen-antibody interaction were measured at different activation times. These results suggest that the adhesion force involved in the CD4 antigen-antibody interaction is highly selective and of high affinity.

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

    Science.gov (United States)

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

    2008-01-01

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

  12. Competition of elastic and adhesive properties of carbon nanotubes anchored to atomic force microscopy tips

    International Nuclear Information System (INIS)

    Bernard, Charlotte; Marsaudon, Sophie; Boisgard, Rodolphe; Aime, Jean-Pierre

    2008-01-01

    In this paper we address the mechanical properties of carbon nanotubes anchored to atomic force microscopy (AFM) tips in a detailed analysis of experimental results and exhaustive description of a simple model. We show that volume elastic and surface adhesive forces both contribute to the dynamical AFM experimental signals. Their respective weights depend on the nanotube properties and on an experimental parameter: the oscillation amplitude. To quantify the elastic and adhesive contributions, a simple analytical model is used. It enables analytical expressions of the resonance frequency shift and dissipation that can be measured in the atomic force microscopy dynamical frequency modulation mode. It includes the nanotube adhesive contribution to the frequency shift. Experimental data for single-wall and multi-wall carbon nanotubes compare well to the model predictions for different oscillation amplitudes. Three parameters can be extracted: the distance necessary to unstick the nanotube from the surface and two spring constants corresponding to tube compression and to the elastic force required to overcome the adhesion force

  13. Coherence and fluctuations in the interaction between moving atoms and a quantum field

    International Nuclear Information System (INIS)

    Hu, B.L.; Raval, A.

    1998-01-01

    Mesoscopic physics deals with three fundamental issues: quantum coherence, fluctuations and correlations. Here we analyze these issues for atom optics, using a simplified model of an assembly of atoms (or detectors, which are particles with some internal degree of freedom) moving in arbitrary trajectories in a quantum field. Employing the influence functional formalism, we study the self-consistent effect of the field on the atoms, and their mutual interactions via coupling to the field. We derive the coupled Langevin equations for the atom assemblage and analyze the relation of dissipative dynamics of the atoms (detectors) with the correlation and fluctuations of the quantum field. This provides a useful theoretical framework for analysing the coherent properties of atom-field systems. (author)

  14. Magnetic field dependent atomic tunneling in non-magnetic glasses

    International Nuclear Information System (INIS)

    Ludwig, S.; Enss, C.; Hunklinger, S.

    2003-01-01

    The low-temperature properties of insulating glasses are governed by atomic tunneling systems (TSs). Recently, strong magnetic field effects in the dielectric susceptibility have been discovered in glasses at audio frequencies at very low temperatures. Moreover, it has been found that the amplitude of two-pulse polarization echoes generated in non-magnetic multi-component glasses at radio frequencies and at very low temperatures shows a surprising non-monotonic magnetic field dependence. The magnitude of the latter effect indicates that virtually all TSs are affected by the magnetic field, not only a small subset of systems. We have studied the variation of the magnetic field dependence of the echo amplitude as a function of the delay time between the two excitation pulses and at different frequencies. Our results indicate that the evolution of the phase of resonant TSs is changed by the magnetic field

  15. Magnetic field dependent atomic tunneling in non-magnetic glasses

    Science.gov (United States)

    Ludwig, S.; Enss, C.; Hunklinger, S.

    2003-05-01

    The low-temperature properties of insulating glasses are governed by atomic tunneling systems (TSs). Recently, strong magnetic field effects in the dielectric susceptibility have been discovered in glasses at audio frequencies at very low temperatures. Moreover, it has been found that the amplitude of two-pulse polarization echoes generated in non-magnetic multi-component glasses at radio frequencies and at very low temperatures shows a surprising non-monotonic magnetic field dependence. The magnitude of the latter effect indicates that virtually all TSs are affected by the magnetic field, not only a small subset of systems. We have studied the variation of the magnetic field dependence of the echo amplitude as a function of the delay time between the two excitation pulses and at different frequencies. Our results indicate that the evolution of the phase of resonant TSs is changed by the magnetic field.

  16. Length-extension resonator as a force sensor for high-resolution frequency-modulation atomic force microscopy in air.

    Science.gov (United States)

    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.

  17. Health physics manpower in the atomic energy field, 1968-2000

    International Nuclear Information System (INIS)

    Baker, J.G.

    1978-01-01

    The structure of employment, historical trends and projections, of health physics workers in the atomic energy field is examined using U.S. Bureau of Labor Statistics survey data. During the 1968 to 1975 period atomic energy field employment has grown at a rate of 4.6% annually, compared to a rate of 1.8% for the U.S. economy. The majority of the growth has been concentrated in the private sector, while government-owned contractor-operated employment declined from 1968 through 1973. Data indicated that growth in the private sector is strongly correlated to growth in nuclear megawatt capacity. The recent revisions in projected generation capacity have depressed considerably the growth in future health physics worker demand. Using the most recent estimates of future capacity, health physics professional requirements in the field are expected to grow at a rate of 7.0% and technician requirements at a rate of 7.4% annually for the period 1975-1985. These results compare favourably with other published studies, all of which project faster growth for technicians than for professionals. (author)

  18. Atoms and Ions Interacting with Particles and Fields: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Robicheaux, Francis [Auburn Univ., AL (United States)

    2014-09-18

    This grant supported research in basic atomic, molecular and optical physics related to the interactions of atoms with particles and fields. The duration of the grant was the 10 year period from 8/2003 to 8/2013. All of the support from the grant was used to pay salaries of the PI, postdocs, graduate students, and undergraduates and travel to conferences and meetings. The results were in the form of publications in peer reviewed journals. There were 65 peer reviewed publications over these 10 years with 8 of the publications in Physical Review Letters; all of the other articles were in respected peer reviewed journals (Physical Review A, New Journal of Physics, Journal of Physics B, ...). I will disuss the results for the periods of time relevant for each grant period.

  19. Free-standing biomimetic polymer membrane imaged with atomic force microscopy

    DEFF Research Database (Denmark)

    Rein, Christian; Pszon-Bartosz, Kamila Justyna; Jensen, Karin Bagger Stibius

    2011-01-01

    Fluid polymeric biomimetic membranes are probed with atomic force microscopy (AFM) using probes with both normal tetrahedrally shaped tips and nanoneedle-shaped Ag2Ga rods. When using nanoneedle probes, the collected force volume data show three distinct membrane regions which match the expected...... membrane structure when spanning an aperture in a hydrophobic scaffold. The method used provides a general method for mapping attractive fluid surfaces. In particular, the nanoneedle probing allows for characterization of free-standing biomimetic membranes with thickness on the nanometer scale suspended...... over 300-μm-wide apertures, where the membranes are stable toward hundreds of nanoindentations without breakage. © 2010 American Chemical Society....

  20. Quantitative compositional analysis and field-evaporation behavior of ordered Ni4Mo on an atomic plane-by-plane basis: an atom-probe field-ion microscope study. MSC report No. 4802

    International Nuclear Information System (INIS)

    Yamamoto, M.; Seidman, D.N.

    1982-10-01

    The (211) fundamental and (101) superlattice planes, of the bct lattice, were analysed chemically on an atomic plane-by-plane basis. It was demonstrated that the composition of each individual plane can be determined as a function of depth without any ambiguity. The overall average Mo concentration was measured to be 17.1 at. % for the (211) fundamental plane. Details of the field evaporation behavior of the (211) fundamental and (101) superlattice planes were studied. The field-evaporation behavior is described in terms of the field-evaporation rate, the order of the field evaporated ions, etc. Each individual atomic plane field evaporated on an atomic plane-by-plane basis for the (211) fundamental plane. While for (101) superlattice plane a group of planes consisting of one plane of Mo atoms and four planes of Ni atoms field-evaporated as a unit. An abnormal increase in the number of Mo atoms was found in the central portion of the (211) fundamental plane. Possible mechanisms for the abnormal field evaporation rate are discussed. It is concluded that the atom probe technique can be used to follow the physics and chemistry of the field-evaporation process and the chemistry of the alloy as a function of position, on a subnanometer scale, throughout the specimen. 13 figures

  1. The Use of Atomic Force Microscopy as a Technique for the Identification of Cancerous Cells

    International Nuclear Information System (INIS)

    Lekka, M.

    2007-11-01

    The monograph presents the use of atomic force microscopy (AFM) as a tool for the identification of cancerous cells by studies of the expression of different types of molecules directly on the surface of living cells. The full quantitative description (that is not accessible by other techniques) performed for a given type of molecular interactions has been obtained by using the following quantities: an unbinding force, probability, rupture length and the effective spring constant taking into account the stiffness of a single complex. All, these parameters were extracted from AFM measurements The analysis of the interaction forces performed by AFM allows the quantitative determination of: i) the static properties of a single molecular complex where its strength of interaction and stiffness of the studied complex can be obtained, ii) dynamic properties, on the basis of which the kinetic properties of the unbinding process can be delivered, and iii) properties of adhesion clusters, where the interrelation between single complexes can be characterized, in particular the mechanism of the unbinding can be obtained. The presented characterization of the interaction force between single molecules demonstrates that atomic force microscopy can be used as exceptional technique to study the expression of molecules on a cell surface. Such measurements are not limited to a typical interactions occurring between single molecules but also it is possible to study the interactions between parts of molecules. The results presented in this monograph point to a novel approach to identify cancer-related changes in a quantitative way what can be used for describing and confirming the pathological state of a single cell. (author)

  2. Communication: atomic force detection of single-molecule nonlinear optical vibrational spectroscopy.

    Science.gov (United States)

    Saurabh, Prasoon; Mukamel, Shaul

    2014-04-28

    Atomic Force Microscopy (AFM) allows for a highly sensitive detection of spectroscopic signals. This has been first demonstrated for NMR of a single molecule and recently extended to stimulated Raman in the optical regime. We theoretically investigate the use of optical forces to detect time and frequency domain nonlinear optical signals. We show that, with proper phase matching, the AFM-detected signals closely resemble coherent heterodyne-detected signals. Applications are made to AFM-detected and heterodyne-detected vibrational resonances in Coherent Anti-Stokes Raman Spectroscopy (χ((3))) and sum or difference frequency generation (χ((2))).

  3. The Closed-Orbit Theory for General Rydberg Atoms in External Fields

    International Nuclear Information System (INIS)

    Carboni, R.

    1997-01-01

    The photoabsorption spectra of hydrogen Rydberg atoms, as well of model Rydberg atoms in pure magnetic or electric fields have been successfully calculated using the semiclassical closed-orbit theory. The theory relates the resonances of the spectra to closed classical orbits of the excited electron. The dynamics of multielectron atoms is more complicated than the hydrogenic one; additionally, when the atoms are in the presence of perpendicular magnetic and electric fields becomes more complex than when they are in pure fields, due to the fact that the Hamiltonian is non-separable in three degrees of freedom, instead of two non-separable degrees of freedom. In this work, I present an extension of the closed-orbit theory to three degrees of freedom, considering arbitrary quantum defects, i.e., general atoms. (Author) [es

  4. Energy shift and Casimir-Polder force for an atom out of thermal equilibrium near a dielectric substrate

    Science.gov (United States)

    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.

  5. Core-electron binding energies from self-consistent field molecular orbital theory using a mixture of all-electron real atoms and valence-electron model atoms

    International Nuclear Information System (INIS)

    Quinn, C.M.; Schwartz, M.E.

    1981-01-01

    The chemistry of large systems such as clusters may be readily investigated by valence-electron theories based on model potentials, but such an approach does not allow for the examination of core-electron binding energies which are commonly measured experimentally for such systems. Here we merge our previously developed Gaussian based valence-electron model potential theory with all-electron ab initio theory to allow for the calculation of core orbital binding energies when desired. For the atoms whose cores are to be examined, we use the real nuclear changes, all of the electrons, and the appropriate many-electron basis sets. For the rest of the system we use reduced nuclear charges, the Gaussian based model potentials, only the valence electrons, and appropriate valence-electron basis sets. Detailed results for neutral Al 2 are presented for the cases of all-electron, mixed real--model, and model--model SCF--MO calculations. Several different all-electron and valence electron calculations have been done to test the use of the model potential per se, as well as the effect of basis set choice. The results are in all cases in excellent agreement with one another. Based on these studies, a set of ''double-zeta'' valence and all-electron basis functions have been used for further SCF--MO studies on Al 3 , Al 4 , AlNO, and OAl 3 . For a variety of difference combinations of real and model atoms we find excellent agreement for relative total energies, orbital energies (both core and valence), and Mulliken atomic populations. Finally, direct core-hole-state ionic calculations are reported in detail for Al 2 and AlNO, and noted for Al 3 and Al 4 . Results for corresponding frozen-orbital energy differences, relaxed SCF--MO energy differences, and relaxation energies are in all cases in excellent agreement (never differing by more than 0.07 eV, usually by somewhat less). The study clearly demonstrates the accuracy of the mixed real--model theory

  6. Multiscale modeling of interaction of alane clusters on Al(111) surfaces : a reactive force field and infrared absorbtion spectroscopy approach

    NARCIS (Netherlands)

    Ojwang, J.G.O.; Chaudhuri, S.; Duin, van A.C.T.; Chabal, Y.J.; Veyan, J.-F.; Santen, van R.A.; Kramer, G.J.; Goddard III, W.A.

    2010-01-01

    We have used reactive force field (ReaxFF) to investigate the mechanism of interaction of alanes on Al(111) surface. Our simulations show that, on the Al(111) surface, alanes oligomerize into larger alanes. In addition, from our simulations, adsorption of atomic hydrogen on Al(111) surface leads to

  7. Polarization contrast in photon scanning tunnelling microscopy combined with atomic force microscopy

    NARCIS (Netherlands)

    Propstra, K.; Propstra, K.; van Hulst, N.F.

    1995-01-01

    Photon scanning tunnelling microscopy combined with atomic force microscopy allows simultaneous acquisition and direct comparison of optical and topographical images, both with a lateral resolution of about 30 nm, far beyond the optical diffraction limit. The probe consists of a modified

  8. Molecular structure of dipalmitoylphospatidylcholine Langmuir-Blodgett monolayers studied by atomic force microscopy.

    NARCIS (Netherlands)

    Zhai, X.; Kleijn, J.M.

    1997-01-01

    Monolayers of dipalmitoylphosphatidylcholine (DPPC) on the air-water interface have been transferred at various surface pressures onto quartz substrates using the Langmuir-Blodgett (LB) technique. The topography of these layers, on a molecular scale, has been examined by atomic force microscopy

  9. Dynamic effect of collision failure of phase in gas of cold dark atoms

    International Nuclear Information System (INIS)

    Il'ichev, L.V.

    2005-01-01

    In a gas of slow atoms exhibiting the effect of coherent population trapping (CPT) on the sublevels of the ground state in a spatially nonuniform light field, rare collisions destroying the CPT state initiate the irreversible exchange of momentum between radiation and atoms. This exchange is manifested as an additional force that acts on the particles. The force is of geometric origin, being determined only by the structure of the field of local CPT states. When this force is not masked by the standard collision change in atomic momentum, the observation of the kinetics of the particles may provide information on the physics of the collisions [ru

  10. Atom collisions in a strong electromagnetic field

    International Nuclear Information System (INIS)

    Smirnov, V.S.; Chaplik, A.V.

    1976-01-01

    It is shown that the long-range part of interatomic interaction is considerably altered in a strong electromagnetic field. Instead of the van der Waals law the potential asymptote can best be described by a dipole-dipole R -3 law. Impact broadening and the line shift in a strong nonresonant field are calculated. The possibility of bound states of two atoms being formed in a strong light field is discussed

  11. Induced forces in the gravitational field

    International Nuclear Information System (INIS)

    Voracek, P.

    1979-01-01

    In this paper the expression for the magnitude of the so-called induced force, acting on a mass particle, is deduced. The origin of this force is causally connected to the increase of the rest mass of the particle in the gravitational field. (orig.)

  12. Noncontact atomic force microscopy in liquid environment with quartz tuning fork and carbon nanotube probe

    DEFF Research Database (Denmark)

    Kageshima, M.; Jensenius, Henriette; Dienwiebel, M.

    2002-01-01

    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 surface were detected both in the frequency shift and dissipation. Due to t...

  13. Air–water interface of submerged superhydrophobic surfaces imaged by atomic force microscopy

    Directory of Open Access Journals (Sweden)

    Markus Moosmann

    2017-08-01

    Full Text Available Underwater air retention of superhydrophobic hierarchically structured surfaces is of increasing interest for technical applications. Persistent air layers (the Salvinia effect are known from biological species, for example, the floating fern Salvinia or the backswimmer Notonecta. The use of this concept opens up new possibilities for biomimetic technical applications in the fields of drag reduction, antifouling, anticorrosion and under water sensing. Current knowledge regarding the shape of the air–water interface is insufficient, although it plays a crucial role with regards to stability in terms of diffusion and dynamic conditions. Optical methods for imaging the interface have been limited to the micrometer regime. In this work, we utilized a nondynamic and nondestructive atomic force microscopy (AFM method to image the interface of submerged superhydrophobic structures with nanometer resolution. Up to now, only the interfaces of nanobubbles (acting almost like solids have been characterized by AFM at these dimensions. In this study, we show for the first time that it is possible to image the air–water interface of submerged hierarchically structured (micro-pillars surfaces by AFM in contact mode. By scanning with zero resulting force applied, we were able to determine the shape of the interface and thereby the depth of the water penetrating into the underlying structures. This approach is complemented by a second method: the interface was scanned with different applied force loads and the height for zero force was determined by linear regression. These methods open new possibilities for the investigation of air-retaining surfaces, specifically in terms of measuring contact area and in comparing different coatings, and thus will lead to the development of new applications.

  14. Molecular dynamics simulation of amplitude modulation atomic force microscopy

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  15. Semiclassical calculation of ionisation rate for Rydberg helium atoms in an electric field

    International Nuclear Information System (INIS)

    Wang De-Hua

    2011-01-01

    The ionisation of Rydberg helium atoms in an electric field above the classical ionisation threshold has been examined using the semiclassical method, with particular emphasis on discussing the influence of the core scattering on the escape dynamics of electrons. The results show that the Rydberg helium atoms ionise by emitting a train of electron pulses. Unlike the case of the ionisation of Rydberg hydrogen atom in parallel electric and magnetic fields, where the pulses of the electron are caused by the external magnetic field, the pulse trains for Rydberg helium atoms are created through core scattering. Each peak in the ionisation rate corresponds to the contribution of one core-scattered combination trajectory. This fact further illustrates that the ionic core scattering leads to the chaotic property of the Rydberg helium atom in external fields. Our studies provide a simple explanation for the escape dynamics in the ionisation of nonhydrogenic atoms in external fields. (atomic and molecular physics)

  16. Classical trajectory perspective of atomic ionization in strong laser fields. Semiclassical modeling

    International Nuclear Information System (INIS)

    Liu, Jie

    2014-01-01

    Dealing with timely and interesting issues in strong laser physics. Illustrates complex strong field atomic ionization with the simple semiclassical model of classical trajectory perspective for the first time. Provides a theoretical model that can be used to account for recent experiments. The ionization of atoms and molecules in strong laser fields is an active field in modern physics and has versatile applications in such as attosecond physics, X-ray generation, inertial confined fusion (ICF), medical science and so on. Classical Trajectory Perspective of Atomic Ionization in Strong Laser Fields covers the basic concepts in this field and discusses many interesting topics using the semiclassical model of classical trajectory ensemble simulation, which is one of the most successful ionization models and has the advantages of a clear picture, feasible computing and accounting for many exquisite experiments quantitatively. The book also presents many applications of the model in such topics as the single ionization, double ionization, neutral atom acceleration and other timely issues in strong field physics, and delivers useful messages to readers with presenting the classical trajectory perspective on the strong field atomic ionization. The book is intended for graduate students and researchers in the field of laser physics, atom molecule physics and theoretical physics. Dr. Jie Liu is a professor of Institute of Applied Physics and Computational Mathematics, China and Peking University.

  17. Towards nano-physiology of insects with atomic force microscopy.

    Science.gov (United States)

    Dokukin, M E; Guz, N V; Sokolov, I

    2011-02-01

    Little study of insects with modern nanotechnology tools has been done so far. Here we use one of such tool, atomic force microscopy (AFM) to study surface oscillations of the ladybird beetles (Hippodamia convergens) measured in different parts of the insect at picometer level. This allows us to record a much broader spectral range of possible surface vibrations (up to several kHz) than the previously studied oscillations due to breathing, heartbeat cycles, coelopulses, etc. (up to 5-10Hz). Here we demonstrate three different ways with which one can identify the origins of the observed peaks - by physical positioning the probe near a specific organ, and by using biological or chemical stimuli. We report on identification of high frequency peaks associated with H. convergens heart, spiracular closer muscles, and oscillations associated with muscles activated while drinking. The method, being a relatively non-invasive technique providing a new type of information, may be useful in developing "nanophysiology" of insects. Copyright © 2010 Elsevier Ltd. All rights reserved.

  18. The influence of physical and physiological cues on atomic force microscopy-based cell stiffness assessment.

    Directory of Open Access Journals (Sweden)

    Yu-Wei Chiou

    Full Text Available Atomic force microscopy provides a novel technique for differentiating the mechanical properties of various cell types. Cell elasticity is abundantly used to represent the structural strength of cells in different conditions. In this study, we are interested in whether physical or physiological cues affect cell elasticity in Atomic force microscopy (AFM-based assessments. The physical cues include the geometry of the AFM tips, the indenting force and the operating temperature of the AFM. All of these cues show a significant influence on the cell elasticity assessment. Sharp AFM tips create a two-fold increase in the value of the effective Young's modulus (E(eff relative to that of the blunt tips. Higher indenting force at the same loading rate generates higher estimated cell elasticity. Increasing the operation temperature of the AFM leads to decreases in the cell stiffness because the structure of actin filaments becomes disorganized. The physiological cues include the presence of fetal bovine serum or extracellular matrix-coated surfaces, the culture passage number, and the culture density. Both fetal bovine serum and the extracellular matrix are critical for cells to maintain the integrity of actin filaments and consequently exhibit higher elasticity. Unlike primary cells, mouse kidney progenitor cells can be passaged and maintain their morphology and elasticity for a very long period without a senescence phenotype. Finally, cell elasticity increases with increasing culture density only in MDCK epithelial cells. In summary, for researchers who use AFM to assess cell elasticity, our results provide basic and significant information about the suitable selection of physical and physiological cues.

  19. The influence of physical and physiological cues on atomic force microscopy-based cell stiffness assessment.

    Science.gov (United States)

    Chiou, Yu-Wei; Lin, Hsiu-Kuan; Tang, Ming-Jer; Lin, Hsi-Hui; Yeh, Ming-Long

    2013-01-01

    Atomic force microscopy provides a novel technique for differentiating the mechanical properties of various cell types. Cell elasticity is abundantly used to represent the structural strength of cells in different conditions. In this study, we are interested in whether physical or physiological cues affect cell elasticity in Atomic force microscopy (AFM)-based assessments. The physical cues include the geometry of the AFM tips, the indenting force and the operating temperature of the AFM. All of these cues show a significant influence on the cell elasticity assessment. Sharp AFM tips create a two-fold increase in the value of the effective Young's modulus (E(eff)) relative to that of the blunt tips. Higher indenting force at the same loading rate generates higher estimated cell elasticity. Increasing the operation temperature of the AFM leads to decreases in the cell stiffness because the structure of actin filaments becomes disorganized. The physiological cues include the presence of fetal bovine serum or extracellular matrix-coated surfaces, the culture passage number, and the culture density. Both fetal bovine serum and the extracellular matrix are critical for cells to maintain the integrity of actin filaments and consequently exhibit higher elasticity. Unlike primary cells, mouse kidney progenitor cells can be passaged and maintain their morphology and elasticity for a very long period without a senescence phenotype. Finally, cell elasticity increases with increasing culture density only in MDCK epithelial cells. In summary, for researchers who use AFM to assess cell elasticity, our results provide basic and significant information about the suitable selection of physical and physiological cues.

  20. Evaluation of the roughness of the surface of porcelain systems with the atomic force microscope

    International Nuclear Information System (INIS)

    Chavarria Rodriguez, Bernal

    2013-01-01

    The surface of a dental ceramic was evaluated and compared with an atomic force microscope after being treated with different systems of polishing. 14 identical ceramic Lava® Zirconia discs were used to test the different polishing systems. 3 polishing systems from different matrix houses were used to polish dental porcelain. The samples were evaluated quantitatively with an atomic force microscope in order to study the real effectiveness of each system, on the roughness average (Ra) and the maximum peak to valley roughness (Ry) of the ceramic surfaces. A considerable reduction of the surface roughness was obtained by applying different polishing systems on the surface of dental ceramics. Very reliable values of Ra and Ry were obtained by making measurements on the structure reproduced by the atomic force microscope. The advanced ceramics of zirconium oxide presented the best physical characteristics and low levels of surface roughness. A smoother surface was achieved with the application of polishing systems, thus demonstrating the reduction of the surface roughness of a dental ceramic [es

  1. Deflection-voltage curve modelling in atomic force microscopy and its use in DC electrostatic manipulation of gold nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Toset, J; Casuso, I; Samitier, J; Gomila, G [Departament d' Electronica, Universitat de Barcelona and Laboratori de Nanobioenginyeria-CREBEC, Parc CientIfic de Barcelona, C/Josep Samitier 1-5, 08028 Barcelona (Spain)

    2007-01-10

    A model of deflection-voltage curves in atomic force microscopy and its use in DC electrostatic nanomanipulation experiments are presented. The proposed model predicts the deflection of the atomic force microscope probe as a function of the applied probe-substrate voltage, as well as the distance and voltage at which the tip collapses irreversibly onto the substrate due to electrostatic forces. The model is verified experimentally and its use in DC electrostatic manipulation of 25 nm radius gold nanoparticles is demonstrated.

  2. Nanomechanical properties of lithiated Si nanowires probed with atomic force microscopy

    International Nuclear Information System (INIS)

    Lee, Hyunsoo; Shin, Weonho; Choi, Jang Wook; Park, Jeong Young

    2012-01-01

    The nanomechanical properties of fully lithiated and pristine Si nanowires (NWs) deposited on a Si substrate were studied with atomic force microscopy (AFM). Si NWs were synthesized using the vapour-liquid-solid process on stainless-steel substrates using an Au catalyst. Fully lithiated Si NWs were obtained using the electrochemical method, followed by drop-casting on a Si substrate. The roughness of the Si NWs, which was derived from AFM images, is greater for the lithiated Si NWs than for the pristine Si NWs. Force spectroscopy was used to study the influence of lithiation on the tip-surface adhesion force. The lithiated Si NWs revealed a smaller tip-surface adhesion force than the Si substrate by a factor of two, while the adhesion force of the Si NWs is similar to that of the Si substrate. Young's modulus, obtained from the force-distance curve, also shows that the pristine Si NWs have a relatively higher value than the lithiated Si NWs due to the elastically soft and amorphous structures of the lithiated region. These results suggest that force spectroscopy can be used to probe the degree of lithiation at nanometer scale during the charging and discharging processes. (paper)

  3. Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

    Science.gov (United States)

    Lee, M.W.; Meuwly, M.

    2013-01-01

    The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

  4. Two-probe atomic-force microscope manipulator and its applications

    Science.gov (United States)

    Zhukov, A. A.; Stolyarov, V. S.; Kononenko, O. V.

    2017-06-01

    We report on a manipulator based on a two-probe atomic force microscope (AFM) with an individual feedback system for each probe. This manipulator works under an upright optical microscope with 3 mm focal distance. The design of the microscope helps us tomanipulate nanowires using the microscope probes as a two-prong fork. The AFM feedback is realized based on the dynamic full-time contact mode. The applications of the manipulator and advantages of its two-probe design are presented.

  5. Two-probe atomic-force microscope manipulator and its applications.

    Science.gov (United States)

    Zhukov, A A; Stolyarov, V S; Kononenko, O V

    2017-06-01

    We report on a manipulator based on a two-probe atomic force microscope (AFM) with an individual feedback system for each probe. This manipulator works under an upright optical microscope with 3 mm focal distance. The design of the microscope helps us tomanipulate nanowires using the microscope probes as a two-prong fork. The AFM feedback is realized based on the dynamic full-time contact mode. The applications of the manipulator and advantages of its two-probe design are presented.

  6. Moessbauer study of the fast magnetization reversal forced in permalloy and invar by an external rf magnetic field

    International Nuclear Information System (INIS)

    Kopcewicz, M.

    1978-01-01

    The effect of fast magnetization reversal leading to fast relaxation of the hyperfine field (collapse effect) forced by an external rf magnetic field is studied using the Moessbauer technique for permalloy and invar. The rf collapse and sideband effects are investigated as a function of external rf field, frequency, and intensity. The collapse of the hfs spectrum through unresolved hfs spectrum, triangular shape to a single line, as well as the formation of sidebands is observed. The rf collapse effect is attributed to the rf forced uniform rotation of internal magnetization which causes fast magnetization reversal leading to fast relaxation of the hyperfine field as a result of which the average field at the Moessbauer nuclei is reduced to zero. The difference of the magnetization reversal process in permalloy and invar are discussed. It is shown that the origin of collapse and sideband effects is totaly different: the collapse effect being of purely magnetic origin while the formation of sidebands is due to the rf induced mechanical vibrations of iron atoms within the sample. It is possible to damp sidebands without affecting the collapse effect. The results obtained show that the application of the rf field to ferromagnetic materials gives a unique possibility to force, simulate, and control the relaxation effects in ferromagnetic materials. (author)

  7. Atom localization via phase and amplitude control of the driving field

    International Nuclear Information System (INIS)

    Ghafoor, Fazal; Qamar, Sajid; Zubairy, M. Suhail

    2002-01-01

    Control of amplitude and phase of the driving field in an atom-field interaction leads towards the strong line narrowing and quenching in the spontaneous emission spectrum. We exploit this fact for the atom localization scheme and achieve a much better spatial resolution in the conditional position probability distribution of the atom. Most importantly the quenching in the spontaneous emission manifests itself in reducing the periodicity in the conditional position probability distribution and hence the uncertainty in a particular position measurement of the single atom by a factor of 2

  8. Noninvasive determination of optical lever sensitivity in atomic force microscopy

    International Nuclear Information System (INIS)

    Higgins, M.J.; Proksch, R.; Sader, J.E.; Polcik, M.; Mc Endoo, S.; Cleveland, J.P.; Jarvis, S.P.

    2006-01-01

    Atomic force microscopes typically require knowledge of the cantilever spring constant and optical lever sensitivity in order to accurately determine the force from the cantilever deflection. In this study, we investigate a technique to calibrate the optical lever sensitivity of rectangular cantilevers that does not require contact to be made with a surface. This noncontact approach utilizes the method of Sader et al. [Rev. Sci. Instrum. 70, 3967 (1999)] to calibrate the spring constant of the cantilever in combination with the equipartition theorem [J. L. Hutter and J. Bechhoefer, Rev. Sci. Instrum. 64, 1868 (1993)] to determine the optical lever sensitivity. A comparison is presented between sensitivity values obtained from conventional static mode force curves and those derived using this noncontact approach for a range of different cantilevers in air and liquid. These measurements indicate that the method offers a quick, alternative approach for the calibration of the optical lever sensitivity

  9. Noninvasive determination of optical lever sensitivity in atomic force microscopy

    Science.gov (United States)

    Higgins, M. J.; Proksch, R.; Sader, J. E.; Polcik, M.; Mc Endoo, S.; Cleveland, J. P.; Jarvis, S. P.

    2006-01-01

    Atomic force microscopes typically require knowledge of the cantilever spring constant and optical lever sensitivity in order to accurately determine the force from the cantilever deflection. In this study, we investigate a technique to calibrate the optical lever sensitivity of rectangular cantilevers that does not require contact to be made with a surface. This noncontact approach utilizes the method of Sader et al. [Rev. Sci. Instrum. 70, 3967 (1999)] to calibrate the spring constant of the cantilever in combination with the equipartition theorem [J. L. Hutter and J. Bechhoefer, Rev. Sci. Instrum. 64, 1868 (1993)] to determine the optical lever sensitivity. A comparison is presented between sensitivity values obtained from conventional static mode force curves and those derived using this noncontact approach for a range of different cantilevers in air and liquid. These measurements indicate that the method offers a quick, alternative approach for the calibration of the optical lever sensitivity.

  10. Note: Fabrication of a fast-response and user-friendly environmental chamber for atomic force microscopes

    Energy Technology Data Exchange (ETDEWEB)

    Ji, Yanfeng; Hui, Fei; Shi, Yuanyuan; Han, Tingting; Song, Xiaoxue; Pan, Chengbin; Lanza, Mario, E-mail: mlanza@suda.edu.cn [Institute of Functional Nano & Soft Materials, Soochow University, Collaborative Innovation Center of Suzhou Nano Science & Technology, 199 Ren-Ai Road, Suzhou 215123 (China)

    2015-10-15

    The atomic force microscope is one of the most widespread tools in science, but many suppliers do not provide a competitive solution to make experiments in controlled atmospheres. Here, we provide a solution to this problem by fabricating a fast-response and user-friendly environmental chamber. We corroborate the correct functioning of the chamber by studying the formation of local anodic oxidation on a silicon sample (biased under opposite polarities), an effect that can be suppressed by measuring in a dry nitrogen atmosphere. The usefulness of this chamber goes beyond the example here presented, and it could be used in many other fields of science, including physics, mechanics, microelectronics, nanotechnology, medicine, and biology.

  11. An atomic coilgun: using pulsed magnetic fields to slow a supersonic beam

    International Nuclear Information System (INIS)

    Narevicius, E; Parthey, C G; Libson, A; Narevicius, J; Chavez, I; Even, U; Raizen, M G

    2007-01-01

    We report the experimental demonstration of a novel method to slow atoms and molecules with permanent magnetic moments using pulsed magnetic fields. In our experiments, we observe the slowing of a supersonic beam of metastable neon from 461.0 ± 7.7 to 403 ± 16 m s -1 in 18 stages, where the slowed peak is clearly separated from the initial distribution. This method has broad applications as it may easily be generalized, using seeding and entrainment into supersonic beams, to all paramagnetic atoms and molecules

  12. Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields.

    Science.gov (United States)

    Matthews, James F; Beckham, Gregg T; Bergenstråhle-Wohlert, Malin; Brady, John W; Himmel, Michael E; Crowley, Michael F

    2012-02-14

    Molecular dynamics simulations of cellulose have recently become more prevalent due to increased interest in renewable energy applications, and many atomistic and coarse-grained force fields exist that can be applied to cellulose. However, to date no systematic comparison between carbohydrate force fields has been conducted for this important system. To that end, we present a molecular dynamics simulation study of hydrated, 36-chain cellulose Iβ microfibrils at room temperature with three carbohydrate force fields (CHARMM35, GLYCAM06, and Gromos 45a4) up to the near-microsecond time scale. Our results indicate that each of these simulated microfibrils diverge from the cellulose Iβ crystal structure to varying degrees under the conditions tested. The CHARMM35 and GLYCAM06 force fields eventually result in structures similar to those observed at 500 K with the same force fields, which are consistent with the experimentally observed high-temperature behavior of cellulose I. The third force field, Gromos 45a4, produces behavior significantly different from experiment, from the other two force fields, and from previously reported simulations with this force field using shorter simulation times and constrained periodic boundary conditions. For the GLYCAM06 force field, initial hydrogen-bond conformations and choice of electrostatic scaling factors significantly affect the rate of structural divergence. Our results suggest dramatically different time scales for convergence of properties of interest, which is important in the design of computational studies and comparisons to experimental data. This study highlights that further experimental and theoretical work is required to understand the structure of small diameter cellulose microfibrils typical of plant cellulose.

  13. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Wenjun, E-mail: wjzheng@buffalo.edu; Glenn, Paul [Department of Physics, University at Buffalo, Buffalo, New York 14260 (United States)

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  14. Surface features on Sahara soil dust particles made visible by atomic force microscope (AFM phase images

    Directory of Open Access Journals (Sweden)

    M. O. Andreae

    2008-10-01

    Full Text Available We show that atomic force microscopy (AFM phase images can reveal surface features of soil dust particles, which are not evident using other microscopic methods. The non-contact AFM method is able to resolve topographical structures in the nanometer range as well as to uncover repulsive atomic forces and attractive van der Waals' forces, and thus gives insight to surface properties. Though the method does not allow quantitative assignment in terms of chemical compound description, it clearly shows deposits of distinguishable material on the surface. We apply this technique to dust aerosol particles from the Sahara collected over the Atlantic Ocean and describe micro-features on the surfaces of such particles.

  15. Evolution of the field quantum entropy and entanglement in a system of multimode light field interacting resonantly with a two-level atom through N_j-degenerate N~Σ-photon process

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The time evolution of the field quantum entropy and entanglement in a system of multi-mode coherent light field resonantly interacting with a two-level atom by de-generating the multi-photon process is studied by utilizing the Von Neumann re-duced entropy theory,and the analytical expressions of the quantum entropy of the multimode field and the numerical calculation results for three-mode field inter-acting with the atom are obtained. Our attention focuses on the discussion of the influences of the initial average photon number,the atomic distribution angle and the phase angle of the atom dipole on the evolution of the quantum field entropy and entanglement. The results obtained from the numerical calculation indicate that: the stronger the quantum field is,the weaker the entanglement between the quan-tum field and the atom will be,and when the field is strong enough,the two sub-systems may be in a disentangled state all the time; the quantum field entropy is strongly dependent on the atomic distribution angle,namely,the quantum field and the two-level atom are always in the entangled state,and are nearly stable at maximum entanglement after a short time of vibration; the larger the atomic dis-tribution angle is,the shorter the time for the field quantum entropy to evolve its maximum value is; the phase angles of the atom dipole almost have no influences on the entanglement between the quantum field and the two-level atom. Entangled states or pure states based on these properties of the field quantum entropy can be prepared.

  16. Atomic Force Microscope Mediated Chromatography

    Science.gov (United States)

    Anderson, Mark S.

    2013-01-01

    The atomic force microscope (AFM) is used to inject a sample, provide shear-driven liquid flow over a functionalized substrate, and detect separated components. This is demonstrated using lipophilic dyes and normal phase chromatography. A significant reduction in both size and separation time scales is achieved with a 25-micron-length column scale, and one-second separation times. The approach has general applications to trace chemical and microfluidic analysis. The AFM is now a common tool for ultra-microscopy and nanotechnology. It has also been demonstrated to provide a number of microfluidic functions necessary for miniaturized chromatography. These include injection of sub-femtoliter samples, fluidic switching, and sheardriven pumping. The AFM probe tip can be used to selectively remove surface layers for subsequent microchemical analysis using infrared and tip-enhanced Raman spectroscopy. With its ability to image individual atoms, the AFM is a remarkably sensitive detector that can be used to detect separated components. These diverse functional components of microfluidic manipulation have been combined in this work to demonstrate AFM mediated chromatography. AFM mediated chromatography uses channel-less, shear-driven pumping. This is demonstrated with a thin, aluminum oxide substrate and a non-polar solvent system to separate a mixture of lipophilic dyes. In conventional chromatographic terms, this is analogous to thin-layer chromatography using normal phase alumina substrate with sheardriven pumping provided by the AFM tip-cantilever mechanism. The AFM detection of separated components is accomplished by exploiting the variation in the localized friction of the separated components. The AFM tip-cantilever provides the mechanism for producing shear-induced flows and rapid pumping. Shear-driven chromatography (SDC) is a relatively new concept that overcomes the speed and miniaturization limitations of conventional liquid chromatography. SDC is based on a

  17. Teleportation of atomic states with a weak coherent cavity field

    Institute of Scientific and Technical Information of China (English)

    Zheng Shi-Biao

    2005-01-01

    A scheme is proposed for the teleportation of an unknown atomic state. The scheme is based on the resonant interaction of atoms with a coherent cavity field. The mean photon-number of the cavity field is much smaller than one and thus the cavity decay can be effectively suppressed. Another adwntage of the scheme is that only one cavity is required.

  18. Sub-half-wavelength atom localization via two standing-wave fields

    International Nuclear Information System (INIS)

    Jin Luling; Sun Hui; Niu Yueping; Gong Shangqing

    2008-01-01

    We propose a scheme for sub-half-wavelength atom localization in a four-level ladder-type atomic system, which is coupled by two classical standing-wave fields. We find that one of the standing-wave fields can help in enhancing the localization precision, and the other is of crucial importance in increasing the detecting probability and leading sub-half-wavelength localization

  19. Quantification of Staphylococcus aureus adhesion forces on various dental restorative materials using atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Merghni, Abderrahmen, E-mail: abderrahmen_merghni@yahoo.fr [Laboratoire des Maladies Transmissibles et Substances biologiquement actives (LR99ES27) Faculté de Pharmacie de Monastir, Université de Monastir (Tunisia); Kammoun, Dorra [Laboratoire de Biomatériaux et Biotechnologie, Faculté de Médecine Dentaire, Monastir (Tunisia); Hentati, Hajer [Laboratoire de Recherche en Santé Orale et Réhabilitation Bucco-Faciale (LR12ES11), Faculté de Médecine Dentaire de Monastir, Université de Monastir (Tunisia); Janel, Sébastien [BioImaging Center Lille-FR3642, Lille (France); Popoff, Michka [Cellular Microbiology and Physics of Infection-CNRS UMR8204, INSERM U1019, Institut Pasteur de Lille, Lille University (France); Lafont, Frank [BioImaging Center Lille-FR3642, Lille (France); Cellular Microbiology and Physics of Infection-CNRS UMR8204, INSERM U1019, Institut Pasteur de Lille, Lille University (France); Aouni, Mahjoub [Laboratoire des Maladies Transmissibles et Substances biologiquement actives (LR99ES27) Faculté de Pharmacie de Monastir, Université de Monastir (Tunisia); Mastouri, Maha [Laboratoire des Maladies Transmissibles et Substances biologiquement actives (LR99ES27) Faculté de Pharmacie de Monastir, Université de Monastir (Tunisia); Laboratoire de Microbiologie, CHU Fattouma Bourguiba de Monastir (Tunisia)

    2016-08-30

    Highlights: • 4 dental restorative materials were characterized for roughness, angle contact water and surface free energy. • AFM adhesion forces of S. aureus to tested materials were achieved in presence and absence of salivary conditioning film. • S. aureus initial adhesion is dependent on the surface free energy and roughness. - Abstract: In the oral cavity dental restorative biomaterials can act as a reservoir for infection with opportunistic Staphylococcus aureus pathogen, which can lead to the occurrence of secondary caries and treatment failures. Our aim was to evaluate the adhesion forces by S. aureus on four dental restorative biomaterials and to correlate this finding to differences in specific surface characteristics. Additionally, the influence of salivary conditioning films in exerted adhesion forces was investigated. The substrate hydrophobicity was measured by goniometer and the surface free energy was calculated using the equilibrium advancing contact angle values of water, formamide, and diiodomethane on the tested surfaces. The surface roughness was determined using atomic force microscope (AFM). Additionally, cell force spectroscopy was achieved to quantify the forces that drive cell-substrate interactions. S. aureus bacterium exerted a considerable adhesion forces on various dental restorative materials, which decreased in the presence of saliva conditioning film. The influence of the surface roughness and free energy in initial adhesion appears to be more important than the effect of hydrophobicity, either in presence or absence of saliva coating. Hence, control of surface properties of dental restorative biomaterials is of crucial importance in preventing the attachment and subsequent the biofilm formation.

  20. Quantification of Staphylococcus aureus adhesion forces on various dental restorative materials using atomic force microscopy

    International Nuclear Information System (INIS)

    Merghni, Abderrahmen; Kammoun, Dorra; Hentati, Hajer; Janel, Sébastien; Popoff, Michka; Lafont, Frank; Aouni, Mahjoub; Mastouri, Maha

    2016-01-01

    Highlights: • 4 dental restorative materials were characterized for roughness, angle contact water and surface free energy. • AFM adhesion forces of S. aureus to tested materials were achieved in presence and absence of salivary conditioning film. • S. aureus initial adhesion is dependent on the surface free energy and roughness. - Abstract: In the oral cavity dental restorative biomaterials can act as a reservoir for infection with opportunistic Staphylococcus aureus pathogen, which can lead to the occurrence of secondary caries and treatment failures. Our aim was to evaluate the adhesion forces by S. aureus on four dental restorative biomaterials and to correlate this finding to differences in specific surface characteristics. Additionally, the influence of salivary conditioning films in exerted adhesion forces was investigated. The substrate hydrophobicity was measured by goniometer and the surface free energy was calculated using the equilibrium advancing contact angle values of water, formamide, and diiodomethane on the tested surfaces. The surface roughness was determined using atomic force microscope (AFM). Additionally, cell force spectroscopy was achieved to quantify the forces that drive cell-substrate interactions. S. aureus bacterium exerted a considerable adhesion forces on various dental restorative materials, which decreased in the presence of saliva conditioning film. The influence of the surface roughness and free energy in initial adhesion appears to be more important than the effect of hydrophobicity, either in presence or absence of saliva coating. Hence, control of surface properties of dental restorative biomaterials is of crucial importance in preventing the attachment and subsequent the biofilm formation.

  1. Rydberg atoms ionization by microwave field and electromagnetic pulses

    International Nuclear Information System (INIS)

    Kaulakys, B.; Vilutis, G.

    1995-01-01

    A simple theory of the Rydberg atoms ionization by electromagnetic pulses and microwave field is presented. The analysis is based on the scale transformation which reduces the number of parameters and reveals the functional dependencies of the processes. It is shown that the observed ionization of Rydberg atoms by subpicosecond electromagnetic pulses scale classically. The threshold electric field required to ionise a Rydberg state may be simply evaluated in the photonic basis approach for the quantum dynamics or from the multiphoton ionization theory

  2. Absorption of resonant electromagnetic radiation in electron-atom collisions

    International Nuclear Information System (INIS)

    Arslanbekov, T.U.; Pazdzerskii, V.A.; Usachenko, V.I.

    1986-01-01

    Nonrelativistic quantum theory is used to study the possibility of amplification of electromagnetic radiation in forced braking scattering of an electron beam on atoms. The interaction of the atom with the electromagnetic field is considered in the resonant approximation. Cases of large and small detuning from resonance are considered. It is shown that for any orientation of the electron beam relative to the field polarization vector, absorption of radiation occurs, with the major contribution being produced by atomic electrons

  3. Combined short scale roughness and surface dielectric function gradient effects on the determination of tip-sample force in atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Gusso, André, E-mail: gusso@metal.eeimvr.uff.br [Departamento de Ciências Exatas-EEIMVR, Universidade Federal Fluminense, Volta Redonda, RJ 27255-125 (Brazil)

    2013-11-11

    The contribution of tip roughness to the van der Waals force between an atomic force microscopy probe tip and the sample is calculated using the multilayer effective medium model, which allows us to consider the relevant case of roughness characterized by correlation length and amplitude in the nanometer scale. The effect of the surface dielectric function gradient is incorporated in the tip-sample force model. It is concluded that for rms roughness in the few nanometers range the effect of short scale tip roughness is quite significant.

  4. Elastic-properties measurement at high temperatures through contact resonance atomic force microscopy

    DEFF Research Database (Denmark)

    Marinello, Francesco; Pezzuolo, Andrea; Carmignato, Simone

    2015-01-01

    fast direct and non-destructive measurement of Young's modulus and related surface parameters.In this work an instrument set up for Contact Resonance Atomic Force Microscopy is proposed, where the sample with is coupled to a heating stage and a piezoelectric transducer directly vibrate the cantilever...

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

    Science.gov (United States)

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

    2013-03-01

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

  6. Influence of Poisson's ratio variation on lateral spring constant of atomic force microscopy cantilevers

    International Nuclear Information System (INIS)

    Yeh, M.-K.; Tai, N.-Ha; Chen, B.-Y.

    2008-01-01

    Atomic force microscopy (AFM) can be used to measure the surface morphologies and the mechanical properties of nanostructures. The force acting on the AFM cantilever can be obtained by multiplying the spring constant of AFM cantilever and the corresponding deformation. To improve the accuracy of force experiments, the spring constant of AFM cantilever must be calibrated carefully. Many methods, such as theoretical equations, the finite element method, and the use of reference cantilever, were reported to obtain the spring constant of AFM cantilevers. For the cantilever made of single crystal, the Poisson's ratio varies with different cantilever-crystal angles. In this paper, the influences of Poisson's ratio variation on the lateral spring constant and axial spring constant of rectangular and V-shaped AFM cantilevers, with different tilt angles and normal forces, were investigated by the finite element analysis. When the cantilever's tilt angle is 20 deg. and the Poisson's ratio varies from 0.02 to 0.4, the finite element results show that the lateral spring constants decrease 11.75% for the rectangular cantilever with 1 μN landing force and decrease 18.60% for the V-shaped cantilever with 50 nN landing force, respectively. The influence of Poisson's ratio variation on axial spring constant is less than 3% for both rectangular and V-shaped cantilevers. As the tilt angle increases, the axial spring constants for rectangular and V-shaped cantilevers decrease substantially. The results obtained can be used to improve the accuracy of the lateral force measurement when using atomic force microscopy

  7. Lipid domain formation and ligand-receptor distribution in lipid bilayer membranes investigated by atomic force microscopy

    DEFF Research Database (Denmark)

    Kaasgaard, Thomas; Mouritsen, O.G.; Jørgensen, K.

    2002-01-01

    A novel experimental technique, based on atomic force microscopy (AFM), is proposed to visualize the lateral organization of membrane systems in the nanometer range. The technique involves the use of a ligand-receptor pair, biotin-avidin, which introduces a height variation on a solid-supported l......A novel experimental technique, based on atomic force microscopy (AFM), is proposed to visualize the lateral organization of membrane systems in the nanometer range. The technique involves the use of a ligand-receptor pair, biotin-avidin, which introduces a height variation on a solid...

  8. Accurate spring constant calibration for very stiff atomic force microscopy cantilevers

    Energy Technology Data Exchange (ETDEWEB)

    Grutzik, Scott J.; Zehnder, Alan T. [Field of Theoretical and Applied Mechanics, Cornell University, Ithaca, New York 14853 (United States); Gates, Richard S.; Gerbig, Yvonne B.; Smith, Douglas T.; Cook, Robert F. [Nanomechanical Properties Group, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899 (United States)

    2013-11-15

    There are many atomic force microscopy (AFM) applications that rely on quantifying the force between the AFM cantilever tip and the sample. The AFM does not explicitly measure force, however, so in such cases knowledge of the cantilever stiffness is required. In most cases, the forces of interest are very small, thus compliant cantilevers are used. A number of methods have been developed that are well suited to measuring low stiffness values. However, in some cases a cantilever with much greater stiffness is required. Thus, a direct, traceable method for calibrating very stiff (approximately 200 N/m) cantilevers is presented here. The method uses an instrumented and calibrated nanoindenter to determine the stiffness of a reference cantilever. This reference cantilever is then used to measure the stiffness of a number of AFM test cantilevers. This method is shown to have much smaller uncertainty than previously proposed methods. An example application to fracture testing of nanoscale silicon beam specimens is included.

  9. Accurate spring constant calibration for very stiff atomic force microscopy cantilevers

    International Nuclear Information System (INIS)

    Grutzik, Scott J.; Zehnder, Alan T.; Gates, Richard S.; Gerbig, Yvonne B.; Smith, Douglas T.; Cook, Robert F.

    2013-01-01

    There are many atomic force microscopy (AFM) applications that rely on quantifying the force between the AFM cantilever tip and the sample. The AFM does not explicitly measure force, however, so in such cases knowledge of the cantilever stiffness is required. In most cases, the forces of interest are very small, thus compliant cantilevers are used. A number of methods have been developed that are well suited to measuring low stiffness values. However, in some cases a cantilever with much greater stiffness is required. Thus, a direct, traceable method for calibrating very stiff (approximately 200 N/m) cantilevers is presented here. The method uses an instrumented and calibrated nanoindenter to determine the stiffness of a reference cantilever. This reference cantilever is then used to measure the stiffness of a number of AFM test cantilevers. This method is shown to have much smaller uncertainty than previously proposed methods. An example application to fracture testing of nanoscale silicon beam specimens is included

  10. Atomic force microscopic imaging of Acanthamoeba castellanii and Balamuthia mandrillaris trophozoites and cysts.

    Science.gov (United States)

    Aqeel, Yousuf; Siddiqui, Ruqaiyyah; Ateeq, Muhammad; Raza Shah, Muhammad; Kulsoom, Huma; Khan, Naveed Ahmed

    2015-01-01

    Light microscopy and electron microscopy have been successfully used in the study of microbes, as well as free-living protists. Unlike light microscopy, which enables us to observe living organisms or the electron microscope which provides a two-dimensional image, atomic force microscopy provides a three-dimensional surface profile. Here, we observed two free-living amoebae, Acanthamoeba castellanii and Balamuthia mandrillaris under the phase contrast inverted microscope, transmission electron microscope and atomic force microscope. Although light microscopy was of lower magnification, it revealed functional biology of live amoebae such as motility and osmoregulation using contractile vacuoles of the trophozoite stage, but it is of limited value in defining the cyst stage. In contrast, transmission electron microscopy showed significantly greater magnification and resolution to reveal the ultra-structural features of trophozoites and cysts including intracellular organelles and cyst wall characteristics but it only produced a snapshot in time of a dead amoeba cell. Atomic force microscopy produced three-dimensional images providing detailed topographic description of shape and surface, phase imaging measuring boundary stiffness, and amplitude measurements including width, height and length of A. castellanii and B. mandrillaris trophozoites and cysts. These results demonstrate the importance of the application of various microscopic methods in the biological and structural characterization of the whole cell, ultra-structural features, as well as surface components and cytoskeleton of protist pathogens. © 2014 The Author(s) Journal of Eukaryotic Microbiology © 2014 International Society of Protistologists.

  11. Atom-Pair Kinetics with Strong Electric-Dipole Interactions.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2017-09-01

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

  13. Mechanical properties of cellulose nanomaterials studied by contact resonance atomic force microscopy

    Science.gov (United States)

    Ryan Wagner; Robert J. Moon; Arvind Raman

    2016-01-01

    Quantification of the mechanical properties of cellulose nanomaterials is key to the development of new cellulose nanomaterial based products. Using contact resonance atomic force microscopy we measured and mapped the transverse elastic modulus of three types of cellulosic nanoparticles: tunicate cellulose nanocrystals, wood cellulose nanocrystals, and wood cellulose...

  14. Interaction potential and repulsive force between atoms whose internuclear separations are small

    International Nuclear Information System (INIS)

    Barbaro, Jacques

    1971-01-01

    The Thomas-Fermi equation is solved for the homonuclear diatomic molecule. The electronic density and electrostatic potential at each point are used to calculate energies and interaction potentials for very small internuclear separation distances. The repulsive force between atoms is derived by means of the virial theorem. (author) [fr

  15. In situ electrochemical atomic force microscope study on graphite electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Hirasawa, K.A.; Sato, Tomohiro; Asahina, Hitoshi; Yamaguchi, Shoji; Mori, Shoichiro [Mitsubishi Chemical Corp., Inashiki, Ibaraki (Japan). Tsukuba Research Center

    1997-04-01

    Interest in the formation of the solid electrolyte interphase (SEI) film on graphite electrodes has increased recently in the quest to improve the performance of lithium-ion batteries. Topographic and frictional changes on the surface of a highly oriented pyrolytic graphite electrode in 1 M LiCiO{sub 4} ethylene carbonate/ethylmethyl carbonate (1:1) electrolyte were examined during charge and discharge by in situ electrochemical atomic force microscopy and friction force microscopy simultaneously in real-time. Solid electrolyte interphase film formation commenced at approximately 2 V vs. Li/Li{sup +} and stable film formation with an island-like morphology was observed below approximately 0.9 V vs. Li/Li{sup +}. Further experiments on a KS-44 graphite/polyvinylidene difluoride binder composite electrode showed similar phenomena.

  16. Atomic force microscopy-based repeated machining theory for nanochannels on silicon oxide surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Z.Q., E-mail: wangzhiqian@sia.cn [State Key Laboratory of Robotics, Shenyang Institute of Automation, CAS, Shenyang 110016 (China); Graduate University of the Chinese Academy of Sciences, Beijing 100049 (China); Jiao, N.D. [State Key Laboratory of Robotics, Shenyang Institute of Automation, CAS, Shenyang 110016 (China); Tung, S. [Department of Mechanical Engineering, University of Arkansas, Fayetteville, AR 72701 (United States); Dong, Z.L. [State Key Laboratory of Robotics, Shenyang Institute of Automation, CAS, Shenyang 110016 (China)

    2011-02-01

    The atomic force microscopy (AFM)-based repeated nanomachining of nanochannels on silicon oxide surfaces is investigated both theoretically and experimentally. The relationships of the initial nanochannel depth vs. final nanochannel depth at a normal force are systematically studied. Using the derived theory and simulation results, the final nanochannel depth can be predicted easily. Meanwhile, if a nanochannel with an expected depth needs to be machined, a right normal force can be selected simply and easily in order to decrease the wear of the AFM tip. The theoretical analysis and simulation results can be effectively used for AFM-based fabrication of nanochannels.

  17. Force fields for silicas and aluminophosphates based on ab initio calculations

    NARCIS (Netherlands)

    Beest, van B.W.H.; Kramer, G.J.; Santen, van R.A.

    1990-01-01

    Authors address the problem of finding interat. force fields for silicas from ab initio calcns. on small clusters. The force field cannot be detd. from cluster data alone; incorporation of bulk-system information into the force field remains essential. Bearing this in mind, authors derive a force

  18. Polythiophenes and fullerene derivatives based donor-acceptor system: topography by atomic force microscopy

    International Nuclear Information System (INIS)

    Marcakova, M. L.; Repovsky, D.; Cik, G.; Velic, D.

    2017-01-01

    The goal of this work is to examine the surface of a polythiophene/fullerene film in order to understand the structure. In this work polythiophene is used as electron donor and fullerene-derivative is used as electron acceptor. Atomic force microscopy (AFM), is an ideal method to study surfaces and nanostructures. Surfaces of fullerene C60 , fullerene-derivates PCBM, polythiophene P12 and a mixture of P12 and PCBM are characterized. In all samples, the average roughness, the arithmetical value of divergence from the high of the surface, is determined concluding that P12 and PCBM mix together well and form a film with specific topography. (authors)

  19. Spectrum of absorption of a weak signal by an atom in a strong field

    International Nuclear Information System (INIS)

    Bakaev, D.S.; Vdovin, Y.A.; Ermachenko, V.M.; Yakovlenko, S.I.

    1985-01-01

    An analysis is made of the spectrum of absorption of a weak probe electromagnetic field by two-level atoms in a strong resonant laser field, undergoing collision with buffer gas atoms. The analysis is made using an approach that allows for the direct influence of a strong electromagnetic field on the dynamics of an elastic collision between an active atom and a buffer gas atom. Rate equations are analyzed for a combined ''atom--strong electromagnetic field'' system (an atom ''dressed'' by the field) allowing for spontaneous and optical collisional transitions, and also for the interaction with the probe field. In the steady-state case, an expression is derived for the electric susceptibility of the medium at the small-signal frequency. This expression contains the rates of the optical collisional transitions that depend nontrivially on the parameters of the strong electromagnetic field. The phenomenological characteristics of optical collisional transitions generally used are only valid at low intensities and for small frequency detunings of the strong electromagnetic field, i.e., in the impact limit

  20. Localization of cesium on montmorillonite surface investigated by frequency modulation atomic force microscopy

    Science.gov (United States)

    Araki, Yuki; Satoh, Hisao; Okumura, Masahiko; Onishi, Hiroshi

    2017-11-01

    Cation exchange of clay mineral is typically analyzed without microscopic study of the clay surfaces. In order to reveal the distribution of exchangeable cations at the clay surface, we performed in situ atomic-scale observations of the surface changes in Na-rich montmorillonite due to exchange with Cs cations using frequency modulation atomic force microscopy (FM-AFM). Lines of protrusion were observed on the surface in aqueous CsCl solution. The amount of Cs of the montmorillonite particles analyzed by energy dispersive X-ray spectrometry was consistent with the ratio of the number of linear protrusions to all protrusions in the FM-AFM images. The results showed that the protrusions represent adsorbed Cs cations. The images indicated that Cs cations at the surface were immobile, and their occupancy remained constant at 10% of the cation sites at the surface with different immersion times in the CsCl solution. This suggests that the mobility and the number of Cs cations at the surface are controlled by the permanent charge of montmorillonite; however, the Cs distribution at the surface is independent of the charge distribution of the inner silicate layer. Our atomic-scale observations demonstrate that surface cations are distributed in different ways in montmorillonite and mica.

  1. 2D atom localization in a four-level tripod system in laser fields

    OpenAIRE

    Ivanov, Vladimir; Rozhdestvensky, Yuri

    2012-01-01

    We propose a scheme for two-dimensional (2D) atom localization in a four-level tripod system under an influence of two orthogonal standing-wave fields. Position information of the atom is retained in the atomic internal states by an additional probe field either of a standing or of a running wave. It is shown that the localization factors depend crucially on the atom-field coupling that results in such spatial structures of populations as spikes, craters and waves. We demonstrate a high-preci...

  2. Robust operation and performance of integrated carbon nanotubes atomic force microscopy probes

    International Nuclear Information System (INIS)

    Rius, G; Clark, I T; Yoshimura, M

    2013-01-01

    We present a complete characterization of carbon nanotubes-atomic force microscopy (CNT-AFM) probes to evaluate the cantilever operation and advanced properties originating from the CNTs. The fabrication consists of silicon probes tip-functionalized with multiwalled CNTs by microwave plasma enhanced chemical vapor deposition. A dedicated methodology has been defined to evaluate the effect of CNT integration into the Si cantilevers. The presence of the CNTs provides enhanced capability for sensing and durability, as demonstrated using dynamic and static modes, e.g. imaging, indentation and force/current characterization.

  3. Plasma effective field theory advertised, then illustrated by e, p, H-atom gas

    International Nuclear Information System (INIS)

    Brown, L.S.

    2001-01-01

    The first part is a lightning fast overview of the application of ideas of modern effective quantum field theory (which originated in elementary particle theory) to plasma physics. An exhaustive account is presented in a long report with L. G. Yaffe which contains all the details set out in a self-contained and pedagogical fashion. The second part shows how the low temperature but dilute limit of the partition function at two-loop order describes a gas of electrons, protons, and hydrogen atoms in their ground state. Hydrogen atoms emerge automatically from the general framework which does not begin with any explicit consideration of atoms. (orig.)

  4. Robust approach to maximize the range and accuracy of force application in atomic force microscopes with nonlinear position-sensitive detectors

    International Nuclear Information System (INIS)

    Silva, E C C M; Vliet, K J van

    2006-01-01

    The atomic force microscope is used increasingly to investigate the mechanical properties of materials via sample displacement under an applied force. However, both the extent of forces attainable and the accuracy of those forces measurements are significantly limited by the optical lever configuration that is commonly used to infer nanoscale deflection of the cantilever. We present a robust and general approach to characterize and compensate for the nonlinearity of the position-sensitive optical device via data processing, requiring no modification of existing instrumentation. We demonstrate that application of this approach reduced the maximum systematic error on the gradient of a force-displacement response from 50% to 5%, and doubled the calibrated force application range. Finally, we outline an experimental protocol that optimizes the use of the quasi-linear range of the most commonly available optical feedback configurations and also accounts for the residual systematic error, allowing the user to benefit from the full detection range of these indirect force sensors

  5. Lateral force calibration in atomic force microscopy: A new lateral force calibration method and general guidelines for optimization

    International Nuclear Information System (INIS)

    Cannara, Rachel J.; Eglin, Michael; Carpick, Robert W.

    2006-01-01

    Proper force calibration is a critical step in atomic and lateral force microscopies (AFM/LFM). The recently published torsional Sader method [C. P. Green et al., Rev. Sci. Instrum. 75, 1988 (2004)] facilitates the calculation of torsional spring constants of rectangular AFM cantilevers by eliminating the need to obtain information or make assumptions regarding the cantilever's material properties and thickness, both of which are difficult to measure. Complete force calibration of the lateral signal in LFM requires measurement of the lateral signal deflection sensitivity as well. In this article, we introduce a complete lateral force calibration procedure that employs the torsional Sader method and does not require making contact between the tip and any sample. In this method, a colloidal sphere is attached to a 'test' cantilever of the same width, but different length and material as the 'target' cantilever of interest. The lateral signal sensitivity is calibrated by loading the colloidal sphere laterally against a vertical sidewall. The signal sensitivity for the target cantilever is then corrected for the tip length, total signal strength, and in-plane bending of the cantilevers. We discuss the advantages and disadvantages of this approach in comparison with the other established lateral force calibration techniques, and make a direct comparison with the 'wedge' calibration method. The methods agree to within 5%. The propagation of errors is explicitly considered for both methods and the sources of disagreement discussed. Finally, we show that the lateral signal sensitivity is substantially reduced when the laser spot is not centered on the detector

  6. Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field

    Directory of Open Access Journals (Sweden)

    Longhua Yang

    2016-09-01

    Full Text Available Cytochrome c oxidase (CcO is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. This article presents parameters for the cofactors of ba3-type CcO that are compatible with the all-atom Amber ff12SB and ff14SB force fields. Specifically, parameters were developed for the CuA pair, heme b, and the dinuclear center that consists of heme a3 and CuB bridged by a hydroperoxo group. The data includes geometries in XYZ coordinate format for cluster models that were employed to compute proton transfer energies and derive bond parameters and point charges for the force field using density functional theory. Also included are the final parameter files that can be employed with the Amber leap program to generate input files for molecular dynamics simulations with the Amber software package. Based on the high resolution (1.8 Å X-ray crystal structure of the ba3-type CcO from Thermus thermophilus (Protein Data Bank ID number PDB: 3S8F, we built a model that is embedded in a POPC lipid bilayer membrane and solvated with TIP3P water molecules and counterions. We provide PDB data files of the initial model and the equilibrated model that can be used for further studies.

  7. Communication: Calculation of interatomic forces and optimization of molecular geometry with auxiliary-field quantum Monte Carlo

    Science.gov (United States)

    Motta, Mario; Zhang, Shiwei

    2018-05-01

    We propose an algorithm for accurate, systematic, and scalable computation of interatomic forces within the auxiliary-field quantum Monte Carlo (AFQMC) method. The algorithm relies on the Hellmann-Feynman theorem and incorporates Pulay corrections in the presence of atomic orbital basis sets. We benchmark the method for small molecules by comparing the computed forces with the derivatives of the AFQMC potential energy surface and by direct comparison with other quantum chemistry methods. We then perform geometry optimizations using the steepest descent algorithm in larger molecules. With realistic basis sets, we obtain equilibrium geometries in agreement, within statistical error bars, with experimental values. The increase in computational cost for computing forces in this approach is only a small prefactor over that of calculating the total energy. This paves the way for a general and efficient approach for geometry optimization and molecular dynamics within AFQMC.

  8. Atomic force microscopic study of the influence of physical stresses on Saccharomyces cerevisiae and Schizosaccharomyces pombe.

    Science.gov (United States)

    Adya, Ashok K; Canetta, Elisabetta; Walker, Graeme M

    2006-01-01

    Morphological changes in the cell surfaces of the budding yeast Saccharomyces cerevisiae (strain NCYC 1681), and the fission yeast Schizosaccharomyces pombe (strain DVPB 1354), in response to thermal and osmotic stresses, were investigated using an atomic force microscope. With this microscope imaging, together with measurements of culture viability and cell size, it was possible to relate topological changes of the cell surface at nanoscale with cellular stress physiology. As expected, when the yeasts were exposed to thermostress or osmostress, their viability together with the mean cell volume decreased in conjunction with the increase in thermal or osmotic shock. Nevertheless, the viability of cells stressed for up to 1 h remained relatively high. For example, viabilities were >50% and >90% for the thermostressed, and >60% and >70% for the osmostressed S. cerevisiae and Schiz. pombe, respectively. Mean cell volume measurements, and bearing and roughness analyses of atomic force microscope images of stressed yeasts indicate that Schiz. pombe may be more resistant to physical stresses than S. cerevisiae. Overall, this study has highlighted the usefulness of atomic force microscope in studies of yeast stress physiology.

  9. Quantitative assessment of contact and non-contact lateral force calibration methods for atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tran Khac, Bien Cuong; Chung, Koo-Hyun, E-mail: khchung@ulsan.ac.kr

    2016-02-15

    Atomic Force Microscopy (AFM) has been widely used for measuring friction force at the nano-scale. However, one of the key challenges faced by AFM researchers is to calibrate an AFM system to interpret a lateral force signal as a quantifiable force. In this study, five rectangular cantilevers were used to quantitatively compare three different lateral force calibration methods to demonstrate the legitimacy and to establish confidence in the quantitative integrity of the proposed methods. The Flat-Wedge method is based on a variation of the lateral output on a surface with flat and changing slopes, the Multi-Load Pivot method is based on taking pivot measurements at several locations along the cantilever length, and the Lateral AFM Thermal-Sader method is based on determining the optical lever sensitivity from the thermal noise spectrum of the first torsional mode with a known torsional spring constant from the Sader method. The results of the calibration using the Flat-Wedge and Multi-Load Pivot methods were found to be consistent within experimental uncertainties, and the experimental uncertainties of the two methods were found to be less than 15%. However, the lateral force sensitivity determined by the Lateral AFM Thermal-Sader method was found to be 8–29% smaller than those obtained from the other two methods. This discrepancy decreased to 3–19% when the torsional mode correction factor for an ideal cantilever was used, which suggests that the torsional mode correction should be taken into account to establish confidence in Lateral AFM Thermal-Sader method. - Highlights: • Quantitative assessment of three lateral force calibration methods for AFM. • Advantages and disadvantages of three different lateral force calibration method. • Implementation of Multi-Load Pivot method as non-contact calibration technique. • The torsional mode correction for Lateral AFM Thermal-Sader method.

  10. Quantitative assessment of contact and non-contact lateral force calibration methods for atomic force microscopy

    International Nuclear Information System (INIS)

    Tran Khac, Bien Cuong; Chung, Koo-Hyun

    2016-01-01

    Atomic Force Microscopy (AFM) has been widely used for measuring friction force at the nano-scale. However, one of the key challenges faced by AFM researchers is to calibrate an AFM system to interpret a lateral force signal as a quantifiable force. In this study, five rectangular cantilevers were used to quantitatively compare three different lateral force calibration methods to demonstrate the legitimacy and to establish confidence in the quantitative integrity of the proposed methods. The Flat-Wedge method is based on a variation of the lateral output on a surface with flat and changing slopes, the Multi-Load Pivot method is based on taking pivot measurements at several locations along the cantilever length, and the Lateral AFM Thermal-Sader method is based on determining the optical lever sensitivity from the thermal noise spectrum of the first torsional mode with a known torsional spring constant from the Sader method. The results of the calibration using the Flat-Wedge and Multi-Load Pivot methods were found to be consistent within experimental uncertainties, and the experimental uncertainties of the two methods were found to be less than 15%. However, the lateral force sensitivity determined by the Lateral AFM Thermal-Sader method was found to be 8–29% smaller than those obtained from the other two methods. This discrepancy decreased to 3–19% when the torsional mode correction factor for an ideal cantilever was used, which suggests that the torsional mode correction should be taken into account to establish confidence in Lateral AFM Thermal-Sader method. - Highlights: • Quantitative assessment of three lateral force calibration methods for AFM. • Advantages and disadvantages of three different lateral force calibration method. • Implementation of Multi-Load Pivot method as non-contact calibration technique. • The torsional mode correction for Lateral AFM Thermal-Sader method.

  11. Simulating evaporation of surface atoms of thorium-alloyed tungsten in strong electronic fields

    International Nuclear Information System (INIS)

    Bochkanov, P.V.; Mordyuk, V.S.; Ivanov, Yu.I.

    1984-01-01

    By the Monte Carlo method simulating evaporation of surface atoms of thorium - alloyed tungsten in strong electric fields is realized. The strongest evaporation of surface atoms of pure tungsten as compared with thorium-alloyed tungsten in the contentration range of thorium atoms in tungsten matrix (1.5-15%) is shown. The evaporation rate increases with thorium atoms concentration. Determined is in relative units the surface atoms evaporation rate depending on surface temperature and electric field stront

  12. Zeroth-order exchange energy as a criterion for optimized atomic basis sets in interatomic force calculations

    International Nuclear Information System (INIS)

    Varandas, A.J.C.

    1980-01-01

    A suggestion is made for using the zeroth-order exchange term, at the one-exchange level, in the perturbation development of the interaction energy as a criterion for optmizing the atomic basis sets in interatomic force calculations. The approach is illustrated for the case of two helium atoms. (orig.)

  13. Time-series observation of the spreading out of microvessel endothelial cells with atomic force microscopy

    International Nuclear Information System (INIS)

    Han Dong; Ma Wanyun; Liao Fulong; Yeh Meiling; Ouyang Zhigang; Sun Yunxu

    2003-01-01

    The spreading out of microvessel endothelial cells plays a key role in angiogenesis and the post-injury healing of endothelial cells. In our study, a physical force applied with an atomic force microscopic (AFM) cantilever tip in contact mode partly broke the peripheral adhesion that just-confluent cultured rat cerebral microvessel endothelial cells had formed with basal structures and resulted in the cells actively withdrawing from the stimulated area. Time-series changes in cell extension were imaged using tapping mode AFM, in conjunction with total internal reflection fluorescence microscopy, intensified charge-coupled device and field emission scanning electron microscopy. We also interpreted phase images of living endothelial cells. The results showed that formation of a fibronectin molecule monolayer is key to the spreading out of the cells. Lamellipods as well as filopods would spread out in temporal and spatial distribution following the formation of fibronectin layer. In addition, a lattice-like meshwork of filopods formed in the regions leading lamellipods, which would possibly provide a fulcrum for the filaments of the cytoskeleton within the leading cell body periphery

  14. Max Auwaerter Price lecture: building and probing atomic structures

    International Nuclear Information System (INIS)

    Ternes, M.

    2008-01-01

    Full text: The control of the geometric, electronic, and magnetic properties of atomic-scale nanostructures is a prerequisite for the understanding and fabrication of new materials and devices. Two routes lead towards this goal: Atomic manipulation of single atoms and molecules by scanning probe microscopy, or patterning using self-assembly. Atomic manipulation has been performed since almost 20 years, but it has been difficult to answer the simple question: how much force does it take to manipulate atoms and molecules on surfaces? To address this question, we used a combined atomic force and scanning tunneling microscope to simultaneously measure the force and the current between an adsorbate and a tip during atomic manipulation. We found that the force it takes to move an atom depends crucially on the binding between adsorbate and surface. Our results indicate that for moving metal atoms on metal surfaces, the lateral force component plays the dominant role. Measuring the forces during manipulation yielded the full potential energy landscape of the tip-sample interaction. Surprisingly, the potential energy barriers are comparable to diffusion barriers, which are obtained in the absence of a probe tip. Furthermore, we used the scanning tunneling microscope to assemble magnetic structures on a thin insulator. We found, that the spin of the atom is influenced by the magnetocrystalline anisotropy of the supporting surface which lifts the spin degeneracy of the ground state and enables the identification of individual atoms. The ground state of atoms with half-integer spin remains always degenerated at zero field due to Kramers theorem. We found that if these states differ by an orbital momentum of m = ±1 the localized spin is screened by the surrounding conducting electrons of the non-magnetic host and form a many-electron spin-singlet at sufficiently low temperature. (author)

  15. Atom probe field ion microscopy and related topics: A bibliography 1991

    International Nuclear Information System (INIS)

    Russell, K.F.; Miller, M.K.

    1993-01-01

    This report contains a bibliography for 1991 on the following topics: Atom probe field ion microscopy; field desorption mass spectrometry; field emission; field ion microscopy; and field emission theory

  16. Strongly correlated states of a small cold-atom cloud from geometric gauge fields

    International Nuclear Information System (INIS)

    Julia-Diaz, B.; Dagnino, D.; Barberan, N.; Guenter, K. J.; Dalibard, J.; Grass, T.; Lewenstein, M.

    2011-01-01

    Using exact diagonalization for a small system of cold bosonic atoms, we analyze the emergence of strongly correlated states in the presence of an artificial magnetic field. This gauge field is generated by a laser beam that couples two internal atomic states, and it is related to Berry's geometrical phase that emerges when an atom follows adiabatically one of the two eigenstates of the atom-laser coupling. Our approach allows us to go beyond the adiabatic approximation, and to characterize the generalized Laughlin wave functions that appear in the strong magnetic-field limit.

  17. Strongly correlated states of a small cold-atom cloud from geometric gauge fields

    Energy Technology Data Exchange (ETDEWEB)

    Julia-Diaz, B. [Dept. ECM, Facultat de Fisica, U. Barcelona, E-08028 Barcelona (Spain); ICFO-Institut de Ciencies Fotoniques, Parc Mediterrani de la Tecnologia, E-08860 Barcelona (Spain); Dagnino, D.; Barberan, N. [Dept. ECM, Facultat de Fisica, U. Barcelona, E-08028 Barcelona (Spain); Guenter, K. J.; Dalibard, J. [Laboratoire Kastler Brossel, CNRS, UPMC, Ecole Normale Superieure, 24 rue Lhomond, F-75005 Paris (France); Grass, T. [ICFO-Institut de Ciencies Fotoniques, Parc Mediterrani de la Tecnologia, E-08860 Barcelona (Spain); Lewenstein, M. [ICFO-Institut de Ciencies Fotoniques, Parc Mediterrani de la Tecnologia, E-08860 Barcelona (Spain); ICREA-Institucio Catalana de Recerca i Estudis Avancats, E-08010 Barcelona (Spain)

    2011-11-15

    Using exact diagonalization for a small system of cold bosonic atoms, we analyze the emergence of strongly correlated states in the presence of an artificial magnetic field. This gauge field is generated by a laser beam that couples two internal atomic states, and it is related to Berry's geometrical phase that emerges when an atom follows adiabatically one of the two eigenstates of the atom-laser coupling. Our approach allows us to go beyond the adiabatic approximation, and to characterize the generalized Laughlin wave functions that appear in the strong magnetic-field limit.

  18. Determination of electrostatic force and its characteristics based on phase difference by amplitude modulation atomic force microscopy

    Science.gov (United States)

    Wang, Kesheng; Cheng, Jia; Yao, Shiji; Lu, Yijia; Ji, Linhong; Xu, Dengfeng

    2016-12-01

    Electrostatic force measurement at the micro/nano scale is of great significance in science and engineering. In this paper, a reasonable way of applying voltage is put forward by taking an electrostatic chuck in a real integrated circuit manufacturing process as a sample, applying voltage in the probe and the sample electrode, respectively, and comparing the measurement effect of the probe oscillation phase difference by amplitude modulation atomic force microscopy. Based on the phase difference obtained from the experiment, the quantitative dependence of the absolute magnitude of the electrostatic force on the tip-sample distance and applied voltage is established by means of theoretical analysis and numerical simulation. The results show that the varying characteristics of the electrostatic force with the distance and voltage at the micro/nano scale are similar to those at the macroscopic scale. Electrostatic force gradually decays with increasing distance. Electrostatic force is basically proportional to the square of applied voltage. Meanwhile, the applicable conditions of the above laws are discussed. In addition, a comparison of the results in this paper with the results of the energy dissipation method shows the two are consistent in general. The error decreases with increasing distance, and the effect of voltage on the error is small.

  19. Interactions of fast molecular ions traversing thin foils. The contribution from field ionized Rydberg atoms in measurements on convoy electrons

    International Nuclear Information System (INIS)

    Gemmell, D.S.

    1983-01-01

    Experiments with fast (MeV) molecular-ion beams offer many attractive possibilities for studying atomic collisions in solids. Of particular value in such experiments is the possibility of determining the force fields (primarily in the induced electric field) that surround ionic fragments traversing a solid. One has the opportunity to evaluate these fields not just at the fragments themselves (as one would, for example, in stopping-power measurements with monatomic projectiles) but in the spatial regions extending out to several Angstroms from the fragment positions. In this paper we give a brief introduction to the subject and present some recent results

  20. Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

    Science.gov (United States)

    Leng, Yongsheng; Krstić, Predrag S.; Wells, Jack C.; Cummings, Peter T.; Dean, David J.

    2005-06-01

    We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as ˜100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.