WorldWideScience

Sample records for dynamic force spectroscopy

  1. Charge-Transfer Complexes Studied by Dynamic Force Spectroscopy

    Directory of Open Access Journals (Sweden)

    Jurriaan Huskens

    2013-03-01

    Full Text Available In this paper, the strength and kinetics of two charge-transfer complexes, naphthol-methylviologen and pyrene-methylviologen, are studied using dynamic force spectroscopy. The dissociation rates indicate an enhanced stability of the pyrene-methylviologen complex, which agrees with its higher thermodynamic stability compared to naphthol-methylviologen complex.

  2. 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.

  3. Investigation of the heparin-thrombin interaction by dynamic force spectroscopy.

    Science.gov (United States)

    Wang, Congzhou; Jin, Yingzi; Desai, Umesh R; Yadavalli, Vamsi K

    2015-06-01

    The interaction between heparin and thrombin is a vital step in the blood (anti)coagulation process. Unraveling the molecular basis of the interactions is therefore extremely important in understanding the mechanisms of this complex biological process. In this study, we use a combination of an efficient thiolation chemistry of heparin, a self-assembled monolayer-based single molecule platform, and a dynamic force spectroscopy to provide new insights into the heparin-thrombin interaction from an energy viewpoint at the molecular scale. Well-separated single molecules of heparin covalently attached to mixed self-assembled monolayers are demonstrated, whereby interaction forces with thrombin can be measured via atomic force microscopy-based spectroscopy. Further these interactions are studied at different loading rates and salt concentrations to directly obtain kinetic parameters. An increase in the loading rate shows a higher interaction force between the heparin and thrombin, which can be directly linked to the kinetic dissociation rate constant (koff). The stability of the heparin/thrombin complex decreased with increasing NaCl concentration such that the off-rate was found to be driven primarily by non-ionic forces. These results contribute to understanding the role of specific and nonspecific forces that drive heparin-thrombin interactions under applied force or flow conditions. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Charge-state dynamics in electrostatic force spectroscopy

    Czech Academy of Sciences Publication Activity Database

    Ondráček, Martin; Hapala, Prokop; Jelínek, Pavel

    2016-01-01

    Roč. 27, č. 27 (2016), 1-13, č. článku 274005. ISSN 0957-4484 R&D Projects: GA ČR(CZ) GA14-02079S Institutional support: RVO:68378271 Keywords : atomic force microscopy * electron tunneling * redox nanoswitches * electrostatic force spectroscopy Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.440, year: 2016

  5. Analysis of dispersive interactions at polymer/TiAlN interfaces by means of dynamic force spectroscopy.

    Science.gov (United States)

    Wiesing, M; de Los Arcos, T; Gebhard, M; Devi, A; Grundmeier, G

    2017-12-20

    The structural and electronic origins of the interactions between polycarbonate and sputter deposited TiAlN were analysed using a combined electron and force spectroscopic approach. Interaction forces were measured by means of dynamic force spectroscopy and the surface polarizability was analysed by X-ray photoelectron valence band spectroscopy. It could be shown that the adhesive interactions between polycarbonate and TiAlN are governed by van der Waals forces. Different surface cleansing and oxidizing treatments were investigated and the effect of the surface chemistry on the force interactions was analysed. Intense surface oxidation resulted in a decreased adhesion force by a factor of two due to the formation of a 2 nm thick Ti 0.21 Al 0.45 O surface oxide layer. The origin of the residual adhesion forces caused by the mixed Ti 0.21 Al 0.45 O surface oxide was clarified by considering the non-retarded Hamaker coefficients as calculated by Lifshitz theory, based on optical data from Reflection Electron Energy Loss Spectroscopy. This disclosed increased dispersion forces of Ti 0.21 Al 0.45 O due to the presence of Ti(iv) ions and related Ti 3d band optical transitions.

  6. Reconsideration of dynamic force spectroscopy analysis of streptavidin-biotin interactions.

    Science.gov (United States)

    Taninaka, Atsushi; Takeuchi, Osamu; Shigekawa, Hidemi

    2010-05-13

    To understand and design molecular functions on the basis of molecular recognition processes, the microscopic probing of the energy landscapes of individual interactions in a molecular complex and their dependence on the surrounding conditions is of great importance. Dynamic force spectroscopy (DFS) is a technique that enables us to study the interaction between molecules at the single-molecule level. However, the obtained results differ among previous studies, which is considered to be caused by the differences in the measurement conditions. We have developed an atomic force microscopy technique that enables the precise analysis of molecular interactions on the basis of DFS. After verifying the performance of this technique, we carried out measurements to determine the landscapes of streptavidin-biotin interactions. The obtained results showed good agreement with theoretical predictions. Lifetimes were also well analyzed. Using a combination of cross-linkers and the atomic force microscope that we developed, site-selective measurement was carried out, and the steps involved in bonding due to microscopic interactions are discussed using the results obtained by site-selective analysis.

  7. Acoustic force spectroscopy

    NARCIS (Netherlands)

    Sitters, G.; Kamsma, D.; Thalhammer, G.; Ritsch-Marte, M.; Peterman, E.J.G.; Wuite, G.J.L.

    2015-01-01

    Force spectroscopy has become an indispensable tool to unravel the structural and mechanochemical properties of biomolecules. Here we extend the force spectroscopy toolbox with an acoustic manipulation device that can exert forces from subpiconewtons to hundreds of piconewtons on thousands of

  8. Analysis of DNA interactions using single-molecule force spectroscopy.

    Science.gov (United States)

    Ritzefeld, Markus; Walhorn, Volker; Anselmetti, Dario; Sewald, Norbert

    2013-06-01

    Protein-DNA interactions are involved in many biochemical pathways and determine the fate of the corresponding cell. Qualitative and quantitative investigations on these recognition and binding processes are of key importance for an improved understanding of biochemical processes and also for systems biology. This review article focusses on atomic force microscopy (AFM)-based single-molecule force spectroscopy and its application to the quantification of forces and binding mechanisms that lead to the formation of protein-DNA complexes. AFM and dynamic force spectroscopy are exciting tools that allow for quantitative analysis of biomolecular interactions. Besides an overview on the method and the most important immobilization approaches, the physical basics of the data evaluation is described. Recent applications of AFM-based force spectroscopy to investigate DNA intercalation, complexes involving DNA aptamers and peptide- and protein-DNA interactions are given.

  9. Numerical analysis of dynamic force spectroscopy using the torsional harmonic cantilever

    International Nuclear Information System (INIS)

    Solares, Santiago D; Hoelscher, Hendrik

    2010-01-01

    A spectral analysis method has been recently introduced by Stark et al (2002 Proc. Natl Acad. Sci. USA 99 8473-8) and implemented by Sahin et al (2007 Nat. Nanotechnol. 2 507-14) using a T-shaped cantilever design, the torsional harmonic cantilever (THC), which is capable of performing simultaneous tapping-mode atomic force microscopy imaging and force spectroscopy. Here we report on numerical simulations of the THC system using a simple dual-mass flexural-torsional model, which is applied in combination with Fourier data processing software to illustrate the spectroscopy process for quality factors corresponding to liquid, air and vacuum environments. We also illustrate the acquisition of enhanced topographical images and deformed surface contours under the application of uniform forces, and compare the results to those obtained with a previously reported linear dual-spring-mass model.

  10. Handbook of Molecular Force Spectroscopy

    CERN Document Server

    Noy, Aleksandr

    2008-01-01

    "...Noy's Handbook of Molecular Force Spectroscopy is both a timely and useful summary of fundamental aspects of molecular force spectroscopy, and I believe it would make a worthwhile addition to any good scientific library. New research groups that are entering this field would be well advisedto study this handbook in detail before venturing into the exciting and challenging world of molecular force spectroscopy." Matthew F. Paige, University of Saskatchewan, Journal of the American Chemical Society Modern materials science and biophysics are increasingly focused on studying and controlling intermolecular interactions on the single-molecule level. Molecular force spectroscopy was developed in the past decade as the result of several unprecedented advances in the capabilities of modern scientific instrumentation, and defines a number of techniques that use mechanical force measurements to study interactions between single molecules and molecular assemblies in chemical and biological systems. Examples of these...

  11. Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor

    Directory of Open Access Journals (Sweden)

    Sandra Posch

    2016-09-01

    Full Text Available We here give information for a deeper understanding of single molecule force spectroscopy (SMFS data through the example of the blood protein von Willebrand factor (VWF. It is also shown, how fitting of rupture forces versus loading rate profiles in the molecular dynamics (MD loading-rate range can be used to demonstrate the qualitative agreement between SMFS and MD simulations. The recently developed model by Bullerjahn, Sturm, and Kroy (BSK was used for this demonstration. Further, Brownian dynamics (BD simulations, which can be utilized to estimate the lifetimes of intramolecular VWF interactions under physiological shear, are described. For interpretation and discussion of the methods and data presented here, we would like to directly point the reader to the related research paper, “Mutual A domain interactions in the force sensing protein von Willebrand Factor” (Posch et al., 2016 [1]. Keywords: Atomic force microscopy, Single molecule force spectroscopy, Molecular dynamics simulation, Brownian dynamics simulation, von Willebrand factor

  12. Improving estimation of kinetic parameters in dynamic force spectroscopy using cluster analysis

    Science.gov (United States)

    Yen, Chi-Fu; Sivasankar, Sanjeevi

    2018-03-01

    Dynamic Force Spectroscopy (DFS) is a widely used technique to characterize the dissociation kinetics and interaction energy landscape of receptor-ligand complexes with single-molecule resolution. In an Atomic Force Microscope (AFM)-based DFS experiment, receptor-ligand complexes, sandwiched between an AFM tip and substrate, are ruptured at different stress rates by varying the speed at which the AFM-tip and substrate are pulled away from each other. The rupture events are grouped according to their pulling speeds, and the mean force and loading rate of each group are calculated. These data are subsequently fit to established models, and energy landscape parameters such as the intrinsic off-rate (koff) and the width of the potential energy barrier (xβ) are extracted. However, due to large uncertainties in determining mean forces and loading rates of the groups, errors in the estimated koff and xβ can be substantial. Here, we demonstrate that the accuracy of fitted parameters in a DFS experiment can be dramatically improved by sorting rupture events into groups using cluster analysis instead of sorting them according to their pulling speeds. We test different clustering algorithms including Gaussian mixture, logistic regression, and K-means clustering, under conditions that closely mimic DFS experiments. Using Monte Carlo simulations, we benchmark the performance of these clustering algorithms over a wide range of koff and xβ, under different levels of thermal noise, and as a function of both the number of unbinding events and the number of pulling speeds. Our results demonstrate that cluster analysis, particularly K-means clustering, is very effective in improving the accuracy of parameter estimation, particularly when the number of unbinding events are limited and not well separated into distinct groups. Cluster analysis is easy to implement, and our performance benchmarks serve as a guide in choosing an appropriate method for DFS data analysis.

  13. 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

  14. High-resolution high-speed dynamic mechanical spectroscopy of cells and other soft materials with the help of atomic force microscopy.

    Science.gov (United States)

    Dokukin, M; Sokolov, I

    2015-07-28

    Dynamic mechanical spectroscopy (DMS), which allows measuring frequency-dependent viscoelastic properties, is important to study soft materials, tissues, biomaterials, polymers. However, the existing DMS techniques (nanoindentation) have limited resolution when used on soft materials, preventing them from being used to study mechanics at the nanoscale. The nanoindenters are not capable of measuring cells, nanointerfaces of composite materials. Here we present a highly accurate DMS modality, which is a combination of three different methods: quantitative nanoindentation (nanoDMA), gentle force and fast response of atomic force microscopy (AFM), and Fourier transform (FT) spectroscopy. This new spectroscopy (which we suggest to call FT-nanoDMA) is fast and sensitive enough to allow DMS imaging of nanointerfaces, single cells, while attaining about 100x improvements on polymers in both spatial (to 10-70 nm) and temporal resolution (to 0.7 s/pixel) compared to the current art. Multiple frequencies are measured simultaneously. The use of 10 frequencies are demonstrated here (up to 300 Hz which is a rather relevant range for biological materials and polymers, in both ambient conditions and liquid). The method is quantitatively verified on known polymers and demonstrated on cells and polymers blends. Analysis shows that FT-nanoDMA is highly quantitative. The FT-nanoDMA spectroscopy can easily be implemented in the existing AFMs.

  15. Force spectroscopy of hepatocytic extracellular matrix components

    Energy Technology Data Exchange (ETDEWEB)

    Yongsunthon, R., E-mail: YongsuntR@Corning.com [Corning Incorporated, SP-FR-01, R1S32D, Corning, NY 14831 (United States); Baker, W.A.; Bryhan, M.D.; Baker, D.E.; Chang, T.; Petzold, O.N.; Walczak, W.J.; Liu, J.; Faris, R.A.; Senaratne, W.; Seeley, L.A.; Youngman, R.E. [Corning Incorporated, SP-FR-01, R1S32D, Corning, NY 14831 (United States)

    2009-07-15

    We present atomic force microscopy and force spectroscopy data of live hepatocytes (HEPG2/C3A liver cell line) grown in Eagle's Minimum Essential Medium, a complex solution of salts and amino acids commonly used for cell culture. Contact-mode imaging and force spectroscopy of this system allowed correlation of cell morphology and extracellular matrix (ECM) properties with substrate properties. Force spectroscopy analysis of cellular 'footprints' indicated that the cells secrete large polymers (e.g., 3.5 {mu}m contour length and estimated MW 1000 kDa) onto their substrate surface. Although definitive identification of the polymers has not yet been achieved, fluorescent-labeled antibody staining has specified the presence of ECM proteins such as collagen and laminin in the cellular footprints. The stretched polymers appear to be much larger than single molecules of known ECM components, such as collagen and heparan sulfate proteoglycan, thus suggesting that the cells create larger entangled, macromolecular structures from smaller components. There is strong evidence which suggests that the composition of the ECM is greatly influenced by the hydrophobicity of the substrate surface, with preferential production and/or adsorption of larger macromolecules on hydrophobic surfaces.

  16. Probing of miniPEGγ-PNA-DNA Hybrid Duplex Stability with AFM Force Spectroscopy.

    Science.gov (United States)

    Dutta, Samrat; Armitage, Bruce A; Lyubchenko, Yuri L

    2016-03-15

    Peptide nucleic acids (PNA) are synthetic polymers, the neutral peptide backbone of which provides elevated stability to PNA-PNA and PNA-DNA hybrid duplexes. It was demonstrated that incorporation of diethylene glycol (miniPEG) at the γ position of the peptide backbone increased the thermal stability of the hybrid duplexes (Sahu, B. et al. J. Org. Chem. 2011, 76, 5614-5627). Here, we applied atomic force microscopy (AFM) based single molecule force spectroscopy and dynamic force spectroscopy (DFS) to test the strength and stability of the hybrid 10 bp duplex. This hybrid duplex consisted of miniPEGγ-PNA and DNA of the same length (γ(MP)PNA-DNA), which we compared to a DNA duplex with a homologous sequence. AFM force spectroscopy data obtained at the same conditions showed that the γ(MP)PNA-DNA hybrid is more stable than the DNA counterpart, 65 ± 15 pN vs 47 ± 15 pN, respectively. The DFS measurements performed in a range of pulling speeds analyzed in the framework of the Bell-Evans approach yielded a dissociation constant, koff ≈ 0.030 ± 0.01 s⁻¹ for γ(MP)PNA-DNA hybrid duplex vs 0.375 ± 0.18 s⁻¹ for the DNA-DNA duplex suggesting that the hybrid duplex is much more stable. Correlating the high affinity of γ(MP)PNA-DNA to slow dissociation kinetics is consistent with prior bulk characterization by surface plasmon resonance. Given the growing interest in γ(MP)PNA as well as other synthetic DNA analogues, the use of single molecule experiments along with computational analysis of force spectroscopy data will provide direct characterization of various modifications as well as higher order structures such as triplexes and quadruplexes.

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

    Science.gov (United States)

    Hu, Xiaotang; Li, Hongbin

    2014-10-01

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

  18. 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

  19. Molecular Force Spectroscopy on Cells

    Science.gov (United States)

    Liu, Baoyu; Chen, Wei; Zhu, Cheng

    2015-04-01

    Molecular force spectroscopy has become a powerful tool to study how mechanics regulates biology, especially the mechanical regulation of molecular interactions and its impact on cellular functions. This force-driven methodology has uncovered a wealth of new information of the physical chemistry of molecular bonds for various biological systems. The new concepts, qualitative and quantitative measures describing bond behavior under force, and structural bases underlying these phenomena have substantially advanced our fundamental understanding of the inner workings of biological systems from the nanoscale (molecule) to the microscale (cell), elucidated basic molecular mechanisms of a wide range of important biological processes, and provided opportunities for engineering applications. Here, we review major force spectroscopic assays, conceptual developments of mechanically regulated kinetics of molecular interactions, and their biological relevance. We also present current challenges and highlight future directions.

  20. Quantifying Young's moduli of protein fibrils and particles with bimodal force spectroscopy.

    Science.gov (United States)

    Gilbert, Jay; Charnley, Mirren; Cheng, Christopher; Reynolds, Nicholas P; Jones, Owen G

    2017-10-19

    Force spectroscopy is a means of obtaining mechanical information of individual nanometer-scale structures in composite materials, such as protein assemblies for use in consumer films or gels. As a recently developed force spectroscopy technique, bimodal force spectroscopy relates frequency shifts in cantilevers simultaneously excited at multiple frequencies to the elastic properties of the contacted material, yet its utility for quantitative characterization of biopolymer assemblies has been limited. In this study, a linear correlation between experimental frequency shift and Young's modulus of polymer films was used to calibrate bimodal force spectroscopy and quantify Young's modulus of two protein nanostructures: β-lactoglobulin fibrils and zein nanoparticles. Cross-sectional Young's modulus of protein fibrils was determined to be 1.6 GPa while the modulus of zein nanoparticles was determined as 854 MPa. Parallel measurement of β-lactoglobulin fibril by a competing pulsed-force technique found a higher cross-sectional Young's modulus, highlighting the importance of comparative calibration against known standards in both pulsed and bimodal force spectroscopies. These findings demonstrate a successful procedure for measuring mechanical properties of individual protein assemblies with potential use in biological or packaging applications using bimodal force spectroscopy.

  1. Resonant Optical Gradient Force Interaction for Nano-Imaging and-Spectroscopy

    Science.gov (United States)

    2016-07-19

    New J. Phys. 18 (2016) 053042 doi:10.1088/1367-2630/18/5/053042 PAPER Resonant optical gradient force interaction for nano-imaging and -spectroscopy...HonghuaUYang andMarkus BRaschke Department of Physics , Department of Chemistry, and JILA,University of Colorado, Boulder, CO80309,USA E-mail...honghua.yang@colorado.edu andmarkus.raschke@colorado.edu Keywords:nano spectroscopy, optical force, near-field optics Abstract The optical gradient force

  2. Sensing of silver nanoparticles on/in endothelial cells using atomic force spectroscopy.

    Science.gov (United States)

    Kolodziejczyk, Agnieszka; Jakubowska, Aleksandra; Kucinska, Magdalena; Wasiak, Tomasz; Komorowski, Piotr; Makowski, Krzysztof; Walkowiak, Bogdan

    2018-05-10

    Endothelial cells, due to their location, are interesting objects for atomic force spectroscopy study. They constitute a barrier between blood and vessel tissues located deeper, and therefore they are the first line of contact with various substances present in blood, eg, drugs or nanoparticles. This work intends to verify whether the mechanical response of immortalized human umbilical vein endothelial cells (EA.hy926), when exposed to silver nanoparticles, as measured using force spectroscopy, could be effectively used as a bio-indicator of the physiological state of the cells. Silver nanoparticles were characterized with transmission electron microscopy and dynamic light scattering techniques. Tetrazolium salt reduction test was used to determine cell viability after treatment with silver nanoparticles. An elasticity of native cells was examined in the Hanks' buffer whereas fixed cells were softly fixed with formaldehyde. Additional aspect of the work is the comparative force spectroscopy utilizing AFM probes of ball-shape and conical geometries, in order to understand what changes in cell elasticity, caused by SNPs, were detectable with each probe. As a supplement to elasticity studies, cell morphology observation by atomic force microscopy and detection of silver nanoparticles inside cells using transmission electron microscopy were also performed. Cells exposed to silver nanoparticles at the highest selected concentrations (3.6 μg/mL, 16 μg/mL) are less elastic. It may be associated with the reorganization of the cellular cytoskeleton and the "strengthening" of the cell cortex caused by presence of silver nanoparticles. This observation does not depend on cell fixation. Agglomerates of silver nanoparticles were observed on the cell membrane as well as inside the cells. Copyright © 2018 John Wiley & Sons, Ltd.

  3. 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.

  4. Compressive Force Spectroscopy: From Living Cells to Single Proteins.

    Science.gov (United States)

    Wang, Jiabin; Liu, Meijun; Shen, Yi; Sun, Jielin; Shao, Zhifeng; Czajkowsky, Daniel Mark

    2018-03-23

    One of the most successful applications of atomic force microscopy (AFM) in biology involves monitoring the effect of force on single biological molecules, often referred to as force spectroscopy. Such studies generally entail the application of pulling forces of different magnitudes and velocities upon individual molecules to resolve individualistic unfolding/separation pathways and the quantification of the force-dependent rate constants. However, a less recognized variation of this method, the application of compressive force, actually pre-dates many of these "tensile" force spectroscopic studies. Further, beyond being limited to the study of single molecules, these compressive force spectroscopic investigations have spanned samples as large as living cells to smaller, multi-molecular complexes such as viruses down to single protein molecules. Correspondingly, these studies have enabled the detailed characterization of individual cell states, subtle differences between seemingly identical viral structures, as well as the quantification of rate constants of functionally important, structural transitions in single proteins. Here, we briefly review some of the recent achievements that have been obtained with compressive force spectroscopy using AFM and highlight exciting areas of its future development.

  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. Force Dynamics of Verb Complementation

    Directory of Open Access Journals (Sweden)

    Jacek Woźny

    2015-12-01

    Full Text Available Force Dynamics of Verb Complementation The concepts of motion and force are both extensively discussed in cognitive linguistics literature. But they are discussed separately. The first usually in the context of ‘motion situations’ (Talmy, Slobin, Zlatev, the other as part of the Force Dynamics framework, which was developed by Talmy. The aim of this paper is twofold: first, to argue that the concepts of force and motion should not be isolated but considered as two inseparable parts of force-motion events. The second goal is to prove that the modified Force Dynamics (force-motion framework can be used for precise characterization of the verb complementation patterns. To this end, a random sample of 50 sentences containing the verb ‘went’ is analyzed, demonstrating the differences between the categories of intensive and intransitive complementation with respect to the linguistically coded parameters of force and motion.

  7. 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.

  8. 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.

  9. 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.

  10. Enhancing dynamic scanning force microscopy in air: as close as possible

    International Nuclear Information System (INIS)

    Palacios-Lidon, E; Perez-Garcia, B; Colchero, J

    2009-01-01

    Frequency modulation dynamic scanning force microscopy has been implemented in ambient conditions using low oscillation amplitudes (<1 nm) to simultaneously record not only topographic but also additional channels of information, in particular contact potential images. The performance of this mode as compared to the conventional amplitude modulation mode is analyzed in detail using a biological molecule, turning yellow mosaic virus RNA, as the model sample. On the basis of scanning force microscopy imaging as well as spectroscopy experiments, we find that for such very small samples the frequency modulation mode is superior since it can be operated with smaller tip-sample interaction, smaller effective tip-sample distance and lower forces. Combined with Kelvin probe microscopy it results not only in considerably higher electrostatic resolution, but also in correct quantitative values for the contact potential as compared to traditional amplitude modulation scanning force microscopy.

  11. Dynamic force spectroscopy of oppositely charged polyelectrolyte brushes

    NARCIS (Netherlands)

    Spruijt, E.; Cohen Stuart, M.A.; Gucht, van der J.

    2010-01-01

    Ion pairing is the main driving force in the formation of polyelectrolyte complexes, which find widespread use in micellar assemblies, drug carriers, and coatings. In this paper we examine the actual ion pairing forces in a polyelectrolyte complex between two oppositely charged polyelectrolyte

  12. Nanopuller-open data acquisition platform for AFM force spectroscopy experiments

    International Nuclear Information System (INIS)

    Pawlak, Konrad; Strzelecki, Janusz

    2016-01-01

    Atomic Force Microscope (AFM) is a widely used tool in force spectroscopy studies. Presently, this instrument is accessible from numerous vendors, albeit commercial solutions are expensive and almost always hardware and software closed. Approaches for open setups were published, as with modern low cost and readily available piezoelectric actuators, data acquisition interfaces and optoelectronic components building such force spectroscopy AFM is relatively easy. However, suitable software to control such laboratory made instrument was not released. Developing it in the lab requires significant time and effort. Our Nanopuller software described in this paper is intended to eliminate this obstacle. With only minimum adjustments this program can be used to control and acquire data with any suitable National Instruments universal digital/analog interface and piezoelectric actuator analog controller, giving significant freedom and flexibility in designing force spectroscopy experiment. Since the full code, written in a graphical LabVIEW environment is available, our Nanopuller can be easily customized. In this paper we describe the program and test its performance in controlling different setups. Successful and accurate force curve acquisition for standard samples (single molecules of I27O reference titin polyprotein and DNA as well as red blood cells) is shown. - Highlights: • We created open data acquisition software for performing Atomic Force Microscopy force measurements with custom laboratory made setups. • The software allows large flexibility in atomic force microscope design with minimum adjustment necessary. • The software is written in LabVIEW, allowing easy customization. • We successfully tested the program on two different hardware configurations by stretching single macromolecules and indenting cells.

  13. Nanopuller-open data acquisition platform for AFM force spectroscopy experiments

    Energy Technology Data Exchange (ETDEWEB)

    Pawlak, Konrad; Strzelecki, Janusz

    2016-05-15

    Atomic Force Microscope (AFM) is a widely used tool in force spectroscopy studies. Presently, this instrument is accessible from numerous vendors, albeit commercial solutions are expensive and almost always hardware and software closed. Approaches for open setups were published, as with modern low cost and readily available piezoelectric actuators, data acquisition interfaces and optoelectronic components building such force spectroscopy AFM is relatively easy. However, suitable software to control such laboratory made instrument was not released. Developing it in the lab requires significant time and effort. Our Nanopuller software described in this paper is intended to eliminate this obstacle. With only minimum adjustments this program can be used to control and acquire data with any suitable National Instruments universal digital/analog interface and piezoelectric actuator analog controller, giving significant freedom and flexibility in designing force spectroscopy experiment. Since the full code, written in a graphical LabVIEW environment is available, our Nanopuller can be easily customized. In this paper we describe the program and test its performance in controlling different setups. Successful and accurate force curve acquisition for standard samples (single molecules of I27O reference titin polyprotein and DNA as well as red blood cells) is shown. - Highlights: • We created open data acquisition software for performing Atomic Force Microscopy force measurements with custom laboratory made setups. • The software allows large flexibility in atomic force microscope design with minimum adjustment necessary. • The software is written in LabVIEW, allowing easy customization. • We successfully tested the program on two different hardware configurations by stretching single macromolecules and indenting cells.

  14. Single-molecule force-conductance spectroscopy of hydrogen-bonded complexes

    Science.gov (United States)

    Pirrotta, Alessandro; De Vico, Luca; Solomon, Gemma C.; Franco, Ignacio

    2017-03-01

    The emerging ability to study physical properties at the single-molecule limit highlights the disparity between what is observable in an ensemble of molecules and the heterogeneous contributions of its constituent parts. A particularly convenient platform for single-molecule studies are molecular junctions where forces and voltages can be applied to individual molecules, giving access to a series of electromechanical observables that can form the basis of highly discriminating multidimensional single-molecule spectroscopies. Here, we computationally examine the ability of force and conductance to inform about molecular recognition events at the single-molecule limit. For this, we consider the force-conductance characteristics of a prototypical class of hydrogen bonded bimolecular complexes sandwiched between gold electrodes. The complexes consist of derivatives of a barbituric acid and a Hamilton receptor that can form up to six simultaneous hydrogen bonds. The simulations combine classical molecular dynamics of the mechanical deformation of the junction with non-equilibrium Green's function computations of the electronic transport. As shown, in these complexes hydrogen bonds mediate transport either by directly participating as a possible transport pathway or by stabilizing molecular conformations with enhanced conductance properties. Further, we observe that force-conductance correlations can be very sensitive to small changes in the chemical structure of the complexes and provide detailed information about the behavior of single molecules that cannot be gleaned from either measurement alone. In fact, there are regions during the elongation that are only mechanically active, others that are only conductance active, and regions where both force and conductance changes as the complex is mechanically manipulated. The implication is that force and conductance provide complementary information about the evolution of molecules in junctions that can be used to

  15. 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.

  16. Antibody-Unfolding and Metastable-State Binding in Force Spectroscopy and Recognition Imaging

    Science.gov (United States)

    Kaur, Parminder; Qiang-Fu; Fuhrmann, Alexander; Ros, Robert; Kutner, Linda Obenauer; Schneeweis, Lumelle A.; Navoa, Ryman; Steger, Kirby; Xie, Lei; Yonan, Christopher; Abraham, Ralph; Grace, Michael J.; Lindsay, Stuart

    2011-01-01

    Force spectroscopy and recognition imaging are important techniques for characterizing and mapping molecular interactions. In both cases, an antibody is pulled away from its target in times that are much less than the normal residence time of the antibody on its target. The distribution of pulling lengths in force spectroscopy shows the development of additional peaks at high loading rates, indicating that part of the antibody frequently unfolds. This propensity to unfold is reversible, indicating that exposure to high loading rates induces a structural transition to a metastable state. Weakened interactions of the antibody in this metastable state could account for reduced specificity in recognition imaging where the loading rates are always high. The much weaker interaction between the partially unfolded antibody and target, while still specific (as shown by control experiments), results in unbinding on millisecond timescales, giving rise to rapid switching noise in the recognition images. At the lower loading rates used in force spectroscopy, we still find discrepancies between the binding kinetics determined by force spectroscopy and those determined by surface plasmon resonance—possibly a consequence of the short tethers used in recognition imaging. Recognition imaging is nonetheless a powerful tool for interpreting complex atomic force microscopy images, so long as specificity is calibrated in situ, and not inferred from equilibrium binding kinetics. PMID:21190677

  17. Features calibration of the dynamic force transducers

    Science.gov (United States)

    Sc., M. Yu Prilepko D.; Lysenko, V. G.

    2018-04-01

    The article discusses calibration methods of dynamic forces measuring instruments. The relevance of work is dictated by need to valid definition of the dynamic forces transducers metrological characteristics taking into account their intended application. The aim of this work is choice justification of calibration method, which provides the definition dynamic forces transducers metrological characteristics under simulation operating conditions for determining suitability for using in accordance with its purpose. The following tasks are solved: the mathematical model and the main measurements equation of calibration dynamic forces transducers by load weight, the main budget uncertainty components of calibration are defined. The new method of dynamic forces transducers calibration with use the reference converter “force-deformation” based on the calibrated elastic element and measurement of his deformation by a laser interferometer is offered. The mathematical model and the main measurements equation of the offered method is constructed. It is shown that use of calibration method based on measurements by the laser interferometer of calibrated elastic element deformations allows to exclude or to considerably reduce the uncertainty budget components inherent to method of load weight.

  18. Atomic force microscopy imaging and single molecule recognition force spectroscopy of coat proteins on the surface of Bacillus subtilis spore.

    Science.gov (United States)

    Tang, Jilin; Krajcikova, Daniela; Zhu, Rong; Ebner, Andreas; Cutting, Simon; Gruber, Hermann J; Barak, Imrich; Hinterdorfer, Peter

    2007-01-01

    Coat assembly in Bacillus subtilis serves as a tractable model for the study of the self-assembly process of biological structures and has a significant potential for use in nano-biotechnological applications. In the present study, the morphology of B. subtilis spores was investigated by magnetically driven dynamic force microscopy (MAC mode atomic force microscopy) under physiological conditions. B. subtilis spores appeared as prolate structures, with a length of 0.6-3 microm and a width of about 0.5-2 microm. The spore surface was mainly covered with bump-like structures with diameters ranging from 8 to 70 nm. Besides topographical explorations, single molecule recognition force spectroscopy (SMRFS) was used to characterize the spore coat protein CotA. This protein was specifically recognized by a polyclonal antibody directed against CotA (anti-CotA), the antibody being covalently tethered to the AFM tip via a polyethylene glycol linker. The unbinding force between CotA and anti-CotA was determined as 55 +/- 2 pN. From the high-binding probability of more than 20% in force-distance cycles it is concluded that CotA locates in the outer surface of B. subtilis spores. Copyright (c) 2007 John Wiley & Sons, Ltd.

  19. Resonant forcing of multidimensional chaotic map dynamics.

    Science.gov (United States)

    Foster, Glenn; Hübler, Alfred W; Dahmen, Karin

    2007-03-01

    We study resonances of chaotic map dynamics. We use the calculus of variations to determine the additive forcing function that induces the largest response. We find that resonant forcing functions complement the separation of nearby trajectories, in that the product of the displacement of nearby trajectories and the resonant forcing is a conserved quantity. As a consequence, the resonant function will have the same periodicity as the displacement dynamics, and if the displacement dynamics is irregular, then the resonant forcing function will be irregular as well. Furthermore, we show that resonant forcing functions of chaotic systems decrease exponentially, where the rate equals the negative of the largest Lyapunov exponent of the unperturbed system. We compare the response to optimal forcing with random forcing and find that the optimal forcing is particularly effective if the largest Lyapunov exponent is significantly larger than the other Lyapunov exponents. However, if the largest Lyapunov exponent is much larger than unity, then the optimal forcing decreases rapidly and is only as effective as a single-push forcing.

  20. Force-detected nanoscale absorption spectroscopy in water at room temperature using an optical trap

    Science.gov (United States)

    Parobek, Alexander; Black, Jacob W.; Kamenetska, Maria; Ganim, Ziad

    2018-04-01

    Measuring absorption spectra of single molecules presents a fundamental challenge for standard transmission-based instruments because of the inherently low signal relative to the large background of the excitation source. Here we demonstrate a new approach for performing absorption spectroscopy in solution using a force measurement to read out optical excitation at the nanoscale. The photoinduced force between model chromophores and an optically trapped gold nanoshell has been measured in water at room temperature. This photoinduced force is characterized as a function of wavelength to yield the force spectrum, which is shown to be correlated to the absorption spectrum for four model systems. The instrument constructed for these measurements combines an optical tweezer with frequency domain absorption spectroscopy over the 400-800 nm range. These measurements provide proof-of-principle experiments for force-detected nanoscale spectroscopies that operate under ambient chemical conditions.

  1. Single molecule force spectroscopy: methods and applications in biology

    International Nuclear Information System (INIS)

    Shen Yi; Hu Jun

    2012-01-01

    Single molecule measurements have transformed our view of biomolecules. Owing to the ability of monitoring the activity of individual molecules, we now see them as uniquely structured, fluctuating molecules that stochastically transition between frequently many substrates, as two molecules do not follow precisely the same trajectory. Indeed, it is this discovery of critical yet short-lived substrates that were often missed in ensemble measurements that has perhaps contributed most to the better understanding of biomolecular functioning resulting from single molecule experiments. In this paper, we give a review on the three major techniques of single molecule force spectroscopy, and their applications especially in biology. The single molecular study of biotin-streptavidin interactions is introduced as a successful example. The problems and prospects of the single molecule force spectroscopy are discussed, too. (authors)

  2. Single-cell force spectroscopy of pili-mediated adhesion

    Science.gov (United States)

    Sullan, Ruby May A.; Beaussart, Audrey; Tripathi, Prachi; Derclaye, Sylvie; El-Kirat-Chatel, Sofiane; Li, James K.; Schneider, Yves-Jacques; Vanderleyden, Jos; Lebeer, Sarah; Dufrêne, Yves F.

    2013-12-01

    Although bacterial pili are known to mediate cell adhesion to a variety of substrates, the molecular interactions behind this process are poorly understood. We report the direct measurement of the forces guiding pili-mediated adhesion, focusing on the medically important probiotic bacterium Lactobacillus rhamnosus GG (LGG). Using non-invasive single-cell force spectroscopy (SCFS), we quantify the adhesion forces between individual bacteria and biotic (mucin, intestinal cells) or abiotic (hydrophobic monolayers) surfaces. On hydrophobic surfaces, bacterial pili strengthen adhesion through remarkable nanospring properties, which - presumably - enable the bacteria to resist high shear forces under physiological conditions. On mucin, nanosprings are more frequent and adhesion forces larger, reflecting the influence of specific pili-mucin bonds. Interestingly, these mechanical responses are no longer observed on human intestinal Caco-2 cells. Rather, force curves exhibit constant force plateaus with extended ruptures reflecting the extraction of membrane nanotethers. These single-cell analyses provide novel insights into the molecular mechanisms by which piliated bacteria colonize surfaces (nanosprings, nanotethers), and offer exciting avenues in nanomedicine for understanding and controlling the adhesion of microbial cells (probiotics, pathogens).

  3. Molecular ions, Rydberg spectroscopy and dynamics

    International Nuclear Information System (INIS)

    Jungen, Ch.

    2015-01-01

    Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering

  4. Molecular ions, Rydberg spectroscopy and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Jungen, Ch. [Laboratoire Aimé Cotton, Université de Paris-Sud, 91405 Orsay (France)

    2015-01-22

    Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.

  5. 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.

  6. 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.

  7. Non-equilibrium umbrella sampling applied to force spectroscopy of soft matter.

    Science.gov (United States)

    Gao, Y X; Wang, G M; Williams, D R M; Williams, Stephen R; Evans, Denis J; Sevick, E M

    2012-02-07

    Physical systems often respond on a timescale which is longer than that of the measurement. This is particularly true in soft matter where direct experimental measurement, for example in force spectroscopy, drives the soft system out of equilibrium and provides a non-equilibrium measure. Here we demonstrate experimentally for the first time that equilibrium physical quantities (such as the mean square displacement) can be obtained from non-equilibrium measurements via umbrella sampling. Our model experimental system is a bead fluctuating in a time-varying optical trap. We also show this for simulated force spectroscopy on a complex soft molecule--a piston-rotaxane.

  8. Single molecule force spectroscopy at high data acquisition: A Bayesian nonparametric analysis

    Science.gov (United States)

    Sgouralis, Ioannis; Whitmore, Miles; Lapidus, Lisa; Comstock, Matthew J.; Pressé, Steve

    2018-03-01

    Bayesian nonparametrics (BNPs) are poised to have a deep impact in the analysis of single molecule data as they provide posterior probabilities over entire models consistent with the supplied data, not just model parameters of one preferred model. Thus they provide an elegant and rigorous solution to the difficult problem encountered when selecting an appropriate candidate model. Nevertheless, BNPs' flexibility to learn models and their associated parameters from experimental data is a double-edged sword. Most importantly, BNPs are prone to increasing the complexity of the estimated models due to artifactual features present in time traces. Thus, because of experimental challenges unique to single molecule methods, naive application of available BNP tools is not possible. Here we consider traces with time correlations and, as a specific example, we deal with force spectroscopy traces collected at high acquisition rates. While high acquisition rates are required in order to capture dwells in short-lived molecular states, in this setup, a slow response of the optical trap instrumentation (i.e., trapped beads, ambient fluid, and tethering handles) distorts the molecular signals introducing time correlations into the data that may be misinterpreted as true states by naive BNPs. Our adaptation of BNP tools explicitly takes into consideration these response dynamics, in addition to drift and noise, and makes unsupervised time series analysis of correlated single molecule force spectroscopy measurements possible, even at acquisition rates similar to or below the trap's response times.

  9. Corticomuscular synchronization with small and large dynamic force output

    Science.gov (United States)

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

    2007-01-01

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

  10. Corticomuscular synchronization with small and large dynamic force output

    Directory of Open Access Journals (Sweden)

    Witte Matthias

    2007-11-01

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

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

    Science.gov (United States)

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

    2016-08-01

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

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

    Science.gov (United States)

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

    2008-02-19

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

  13. 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.

  14. Investigation of specific interactions between T7 promoter and T7 RNA polymerase by force spectroscopy using atomic force microscope.

    Science.gov (United States)

    Zhang, Xiaojuan; Yao, Zhixuan; Duan, Yanting; Zhang, Xiaomei; Shi, Jinsong; Xu, Zhenghong

    2018-01-11

    The specific recognition and binding of promoter and RNA polymerase is the first step of transcription initiation in bacteria and largely determines transcription activity. Therefore, direct analysis of the interaction between promoter and RNA polymerase in vitro may be a new strategy for promoter characterization, to avoid interference due to the cell's biophysical condition and other regulatory elements. In the present study, the specific interaction between T7 promoter and T7 RNA polymerase was studied as a model system using force spectroscopy based on atomic force microscope (AFM). The specific interaction between T7 promoter and T7 RNA polymerase was verified by control experiments, and the rupture force in this system was measured as 307.2 ± 6.7 pN. The binding between T7 promoter mutants with various promoter activities and T7 RNA polymerase was analyzed. Interaction information including rupture force, rupture distance and binding percentage were obtained in vitro , and reporter gene expression regulated by these promoters was also measured according to a traditional promoter activity characterization method in vivo Using correlation analysis, it was found that the promoter strength characterized by reporter gene expression was closely correlated with rupture force and the binding percentage by force spectroscopy. These results indicated that the analysis of the interaction between promoter and RNA polymerase using AFM-based force spectroscopy was an effective and valid approach for the quantitative characterization of promoters. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  15. Molecular dynamics simulation of nonlinear spectroscopies of intermolecular motions in liquid water.

    Science.gov (United States)

    Yagasaki, Takuma; Saito, Shinji

    2009-09-15

    Water is the most extensively studied of liquids because of both its ubiquity and its anomalous thermodynamic and dynamic properties. The properties of water are dominated by hydrogen bonds and hydrogen bond network rearrangements. Fundamental information on the dynamics of liquid water has been provided by linear infrared (IR), Raman, and neutron-scattering experiments; molecular dynamics simulations have also provided insights. Recently developed higher-order nonlinear spectroscopies open new windows into the study of the hydrogen bond dynamics of liquid water. For example, the vibrational lifetimes of stretches and a bend, intramolecular features of water dynamics, can be accurately measured and are found to be on the femtosecond time scale at room temperature. Higher-order nonlinear spectroscopy is expressed by a multitime correlation function, whereas traditional linear spectroscopy is given by a one-time correlation function. Thus, nonlinear spectroscopy yields more detailed information on the dynamics of condensed media than linear spectroscopy. In this Account, we describe the theoretical background and methods for calculating higher order nonlinear spectroscopy; equilibrium and nonequilibrium molecular dynamics simulations, and a combination of both, are used. We also present the intermolecular dynamics of liquid water revealed by fifth-order two-dimensional (2D) Raman spectroscopy and third-order IR spectroscopy. 2D Raman spectroscopy is sensitive to couplings between modes; the calculated 2D Raman signal of liquid water shows large anharmonicity in the translational motion and strong coupling between the translational and librational motions. Third-order IR spectroscopy makes it possible to examine the time-dependent couplings. The 2D IR spectra and three-pulse photon echo peak shift show the fast frequency modulation of the librational motion. A significant effect of the translational motion on the fast frequency modulation of the librational motion is

  16. The semiclassical way to dynamics and spectroscopy

    CERN Document Server

    Heller, Eric

    2018-01-01

    Physical systems have been traditionally described in terms of either classical or quantum mechanics. But in recent years, semiclassical methods have developed rapidly, providing deep physical insight and computational tools for quantum dynamics and spectroscopy. In this book, Eric Heller introduces and develops this subject, demonstrating its power with many examples. In the first half of the book, Heller covers relevant aspects of classical mechanics, building from them the semiclassical way through the semiclassical limit of the Feynman path integral. The second half of the book applies this approach to various kinds of spectroscopy, such as molecular spectroscopy and electron imaging and quantum dynamical systems with an emphasis on tunneling. Adopting a distinctly time-dependent viewpoint, Heller argues for semiclassical theories from experimental and theoretical vantage points valuable to research in physics and chemistry. Featuring more than two hundred figures, the book provides a geometric, phase-sp...

  17. Hooke: an open software platform for force spectroscopy.

    Science.gov (United States)

    Sandal, Massimo; Benedetti, Fabrizio; Brucale, Marco; Gomez-Casado, Alberto; Samorì, Bruno

    2009-06-01

    Hooke is an open source, extensible software intended for analysis of atomic force microscope (AFM)-based single molecule force spectroscopy (SMFS) data. We propose it as a platform on which published and new algorithms for SMFS analysis can be integrated in a standard, open fashion, as a general solution to the current lack of a standard software for SMFS data analysis. Specific features and support for file formats are coded as independent plugins. Any user can code new plugins, extending the software capabilities. Basic automated dataset filtering and semi-automatic analysis facilities are included. Software and documentation are available at (http://code.google.com/p/hooke). Hooke is a free software under the GNU Lesser General Public License.

  18. Elastin-like Polypeptide Linkers for Single-Molecule Force Spectroscopy.

    Science.gov (United States)

    Ott, Wolfgang; Jobst, Markus A; Bauer, Magnus S; Durner, Ellis; Milles, Lukas F; Nash, Michael A; Gaub, Hermann E

    2017-06-27

    Single-molecule force spectroscopy (SMFS) is by now well established as a standard technique in biophysics and mechanobiology. In recent years, the technique has benefitted greatly from new approaches to bioconjugation of proteins to surfaces. Indeed, optimized immobilization strategies for biomolecules and refined purification schemes are being steadily adapted and improved, which in turn has enhanced data quality. In many previously reported SMFS studies, poly(ethylene glycol) (PEG) was used to anchor molecules of interest to surfaces and/or cantilever tips. The limitation, however, is that PEG exhibits a well-known trans-trans-gauche to all-trans transition, which results in marked deviation from standard polymer elasticity models such as the worm-like chain, particularly at elevated forces. As a result, the assignment of unfolding events to protein domains based on their corresponding amino acid chain lengths is significantly obscured. Here, we provide a solution to this problem by implementing unstructured elastin-like polypeptides as linkers to replace PEG. We investigate the suitability of tailored elastin-like polypeptides linkers and perform direct comparisons to PEG, focusing on attributes that are critical for single-molecule force experiments such as linker length, monodispersity, and bioorthogonal conjugation tags. Our results demonstrate that by avoiding the ambiguous elastic response of mixed PEG/peptide systems and instead building the molecular mechanical systems with only a single bond type with uniform elastic properties, we improve data quality and facilitate data analysis and interpretation in force spectroscopy experiments. The use of all-peptide linkers allows alternative approaches for precisely defining elastic properties of proteins linked to surfaces.

  19. Probing molecular interactions in bone biomaterials: Through molecular dynamics and Fourier transform infrared spectroscopy

    International Nuclear Information System (INIS)

    Bhowmik, Rahul; Katti, Kalpana S.; Verma, Devendra; Katti, Dinesh R.

    2007-01-01

    Polymer-hydroxyapatite (HAP) composites are widely investigated for their potential use as bone replacement materials. The molecular interactions at mineral polymer interface are known to have significant role of mechanical response of the composite system. Modeling interactions between such dissimilar molecules using molecular dynamics (MD) is an area of current interest. Molecular dynamics studies require potential function or force field parameters. Some force fields are described in literature that represents the structure of hydroxyapatite reasonably well. Yet, the applicability of these force fields for studying the interaction between dissimilar materials (such as mineral and polymer) is limited, as there is no accurate representation of polymer in these force fields. We have obtained the parameters of consistent valence force field (CVFF) for monoclinic hydroxyapatite. Validation of parameters was done by comparing the computationally obtained unit cell parameters, vibrational spectra and atomic distances with XRD and FTIR experiments. Using the obtained parameters of HAP, and available parameters of polymer (polyacrylic acid), interaction study was performed with MD simulations. The MD simulations showed that several hydrogen bonds may form between HAP and polyacrylic acid depending upon the exposed surface of HAP. Also there are some favourable planes of HAP where polyacrylic acid is most likely to attach. We have also simulated the mineralization of HAP using a 'synthetic biomineralization'. These modeling studies are supported by photoacoustic spectroscopy experiments on both porous and non porous composite samples for potential joint replacement and bone tissue engineering applications

  20. Dynamic force microscopy with quartz tuning forks at high oscillation amplitudes

    International Nuclear Information System (INIS)

    Labardi, M

    2007-01-01

    Dynamic force microscopy (DFM) with the self-oscillator (SO) method allows reasonably high scanning rates even with high Q-factors of the resonant force sensor, typical of cantilevers in ultra-high vacuum and of quartz tuning forks. However, due to simpler interpretation of force spectroscopy measurements, small oscillation amplitudes (sub-nm level) are generally preferred. In applications like 'apertureless' scanning near-field optical microscopy (SNOM), oscillation amplitudes of the order of 5-10 nm are needed to increase optical sensitivity and to apply standard optical artefact suppression methods. This motivates the study of the behaviour of tuning forks driven at such high amplitudes, as compared to usual air-operated cantilevers. Both constant-excitation-amplitude (CE) and constant-oscillation-amplitude (CA) modes of SO-DFM are analysed, since the CA mode is more convenient for SNOM applications, denoting remarkable differences. In particular, possible instability effects, previously found in CE mode, are not anticipated for CA mode. It is shown how resonance and approach ('isophase') curves in both modes can be conveniently described in terms of the usual 'normalized frequency shift' γ and of a 'normalized gain' η, defined as a measurement of surface dissipation

  1. Probing the nanoscale interaction forces and elastic properties of organic and inorganic materials using force-distance (F-D) spectroscopy

    Science.gov (United States)

    Vincent, Abhilash

    Due to their therapeutic applications such as radical scavenging, MRI contrast imaging, Photoluminescence imaging, drug delivery, etc., nanoparticles (NPs) have a significant importance in bio-nanotechnology. The reason that prevents the utilizing NPs for drug delivery in medical field is mostly due to their biocompatibility issues (incompatibility can lead to toxicity and cell death). Changes in the surface conditions of NPs often lead to NP cytotoxicity. Investigating the role of NP surface properties (surface charges and surface chemistry) on their interactions with biomolecules (Cells, protein and DNA) could enhance the current understanding of NP cytotoxicity. Hence, it is highly beneficial to the nanotechnology community to bring more attention towards the enhancement of surface properties of NPs to make them more biocompatible and less toxic to biological systems. Surface functionalization of NPs using specific ligand biomolecules have shown to enhance the protein adsorption and cellular uptake through more favorable interaction pathways. Cerium oxide NPs (CNPs also known as nanoceria) are potential antioxidants in cell culture models and understanding the nature of interaction between cerium oxide NPs and biological proteins and cells are important due to their therapeutic application (especially in site specific drug delivery systems). The surface charges and surface chemistry of CNPs play a major role in protein adsorption and cellular uptake. Hence, by tuning the surface charges and by selecting proper functional molecules on the surface, CNPs exhibiting strong adhesion to biological materials can be prepared. By probing the nanoscale interaction forces acting between CNPs and protein molecules using Atomic Force Microscopy (AFM) based force-distance (F-D) spectroscopy, the mechanism of CNP-protein adsorption and CNP cellular uptake can be understood more quantitatively. The work presented in this dissertation is based on the application of AFM in

  2. Classical description of dynamical many-body systems with central forces, spin-orbit forces and spin-spin forces

    International Nuclear Information System (INIS)

    Goepfert, A.

    1994-01-01

    This thesis develops a new model, and related numerical methods, to describe classical time-dependent many-body systems interacting through central forces, spin-orbit forces and spin-spin forces. The model is based on two-particle interactions. The two-body forces consist of attractive and repulsive parts. In this model the investigated multi-particle systems are self-bound. Also the total potential of the whole ensemble is derived from the two-particle potential and is not imposed 'from outside'. Each particle has the three degrees of freedom of its centre-of-mass motion and the spin degree of freedom. The model allows for the particles to be either charged or uncharged. Furthermore, each particle has an angular momentum, an intrinsic spin, and a magnetic dipole moment. Through the electromagnetic forces between these charges and moments there arise dynamical couplings between them. The internal interactions between the charges and moments are well described by electromagnetic coupling mechanisms. In fact, compared to conventional classical molecular dynamics calculations in van der Waals clusters, which have no spin degrees of freedom, or for Heisenberg spin Systems, which have no orbital degrees of freedom, the model presented here contains both types of degrees of freedom with a highly non-trivial coupling. The model allows to study the fundamental effects resulting from the dynamical coupling of the spin and the orbital-motion sub-systems. In particular, the dynamics of the particle mass points show a behaviour basically different from the one of particles in a potential with only central forces. Furthermore, a special type of quenching procedure was invented, which tends to drive the multi-particle Systems into states with highly periodic, non-ergodic behaviour. Application of the model to cluster simulations has provided evidence that the model can also be used to investigate items like solid-to-liquid phase transitions (melting), isomerism and specific heat

  3. 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.

  4. Force spectroscopy of membrane hardness of SH-SY5Y neuroblastoma cells before and after differentiation

    Science.gov (United States)

    Kwon, Sangwoo; Yang, Woochul; Choi, Yun Kyong; Park, Jung Keuck

    2014-05-01

    Atomic force microscopy (AFM) is utilized in many studies for measuring the structure and the physical characteristics of soft and bio materials. In particular, the force spectroscopy function in the AFM system allows us to explore the mechanical properties of bio cells. In this study, we probe the variation in the membrane hardness of human neuroblastoma SH-SY5Y cells (SH-cells) before and after differentiation by using force spectroscopy. The SH-cell, which is usually differentiated by using a chemical treatment with retinoic acid (RA), is a neuronal cell line employed widely as an in-vitro model for neuroscience research. In force spectroscopy, the force-distance curves are obtained from both the original and the RA-treated cells while the AFM tip approaches and pushes on the cell membranes. The slope deduced from linear region in the force-distance curve is the spring constant and corresponds to the hardness of the cell membrane. The spring constant of the RA-treated cells (0.597 ± 0.010 nN/nm) was smaller than that of the original cells (0.794 ± 0.010 nN/nm), reflecting a hardness decrease in the cells differentiated with the RA treatments. The results clearly demonstrated that the differentiated cells are softer than the original cells. The change in the elasticity of the differentiated cells might be caused by morphological modification during differentiation process. We suggest that force spectroscopy can be employed as a novel method to determine the degree of differentiation of stem cells into various functional cells.

  5. Effect of the Magnus force on skyrmion relaxation dynamics

    Science.gov (United States)

    Brown, Barton L.; Täuber, Uwe C.; Pleimling, Michel

    2018-01-01

    We perform systematic Langevin molecular dynamics simulations of interacting skyrmions in thin films. The interplay between the Magnus force, the repulsive skyrmion-skyrmion interaction, and the thermal noise yields different regimes during nonequilibrium relaxation. In the noise-dominated regime, the Magnus force enhances the disordering effects of the thermal noise. In the Magnus-force-dominated regime, the Magnus force cooperates with the skyrmion-skyrmion interaction to yield a dynamic regime with slow decaying correlations. These two regimes are characterized by different values of the aging exponent. In general, the Magnus force accelerates the approach to the steady state.

  6. 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.

  7. Waiting Time Dynamics in Two-Dimensional Infrared Spectroscopy

    NARCIS (Netherlands)

    Jansen, Thomas L. C.; Knoester, Jasper

    We review recent work on the waiting time dynamics of coherent two-dimensional infrared (2DIR) spectroscopy. This dynamics can reveal chemical and physical processes that take place on the femto- and picosecond time scale, which is faster than the time scale that may be probed by, for example,

  8. Investigation of polyelectrolyte desorption by single molecule force spectroscopy

    International Nuclear Information System (INIS)

    Friedsam, C; Seitz, M; Gaub, H E

    2004-01-01

    Single molecule force spectroscopy has evolved into a powerful method for the investigation of intra- and intermolecular interactions at the level of individual molecules. Many examples, including the investigation of the dynamic properties of complex biological systems as well as the properties of covalent bonds or intermolecular transitions within individual polymers, are reported in the literature. The technique has recently been extended to the systematic investigation of desorption processes of individual polyelectrolyte molecules adsorbed on generic surfaces. The stable covalent attachment of polyelectrolyte molecules to the AFM-tip provides the possibility of performing long-term measurements with the same set of molecules and therefore allows the in situ observation of the impact of environmental changes on the adsorption behaviour of individual molecules. Different types of interactions, e.g. electrostatic or hydrophobic interactions, that determine the adsorption process could be identified and characterized. The experiments provided valuable details that help to understand the nature and the properties of non-covalent interactions, which is helpful with regard to biological systems as well as for technical applications. Apart from this, desorption experiments can be utilized to characterize the properties of surfaces or polymer coatings. Therefore they represent a versatile tool that can be further developed in terms of various aspects

  9. Software for Correcting the Dynamic Error of Force Transducers

    Directory of Open Access Journals (Sweden)

    Naoki Miyashita

    2014-07-01

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

  10. Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Yu, H.G.; Muckerman, J.T.

    2010-06-01

    The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.

  11. The effect of the Magnus force on skyrmion relaxation dynamics

    OpenAIRE

    Brown, Barton L.; Täuber, Uwe C.; Pleimling, Michel

    2018-01-01

    We perform systematic Langevin molecular dynamics simulations of interacting skyrmions in thin films. The interplay between Magnus force, repulsive skyrmion-skyrmion interaction and thermal noise yields different regimes during non-equilibrium relaxation. In the noise-dominated regime the Magnus force enhances the disordering effects of the thermal noise. In the Magnus-force-dominated regime, the Magnus force cooperates with the skyrmion-skyrmion interaction to yield a dynamic regime with slo...

  12. 2012 ELECTRONIC SPECTROSCOPY & DYNAMICS GORDON RESEARCH CONFERENCE, JULY 22-27, 2012

    Energy Technology Data Exchange (ETDEWEB)

    Kohler, Bern

    2012-07-27

    Topics covered in this GRC include high-resolution spectroscopy, coherent electronic energy transport in biology, excited state theory and dynamics, excitonics, electronic spectroscopy of cold and ultracold molecules, and the spectroscopy of nanostructures. Several sessions will highlight innovative techniques such as time-resolved x-ray spectroscopy, frequency combs, and liquid microjet photoelectron spectroscopy that have forged stimulating new connections between gas-phase and condensed-phase work.

  13. Medical applications of atomic force microscopy and Raman spectroscopy.

    Science.gov (United States)

    Choi, Samjin; Jung, Gyeong Bok; Kim, Kyung Sook; Lee, Gi-Ja; Park, Hun-Kuk

    2014-01-01

    This paper reviews the recent research and application of atomic force microscopy (AFM) and Raman spectroscopy techniques, which are considered the multi-functional and powerful toolkits for probing the nanostructural, biomechanical and physicochemical properties of biomedical samples in medical science. We introduce briefly the basic principles of AFM and Raman spectroscopy, followed by diagnostic assessments of some selected diseases in biomedical applications using them, including mitochondria isolated from normal and ischemic hearts, hair fibers, individual cells, and human cortical bone. Finally, AFM and Raman spectroscopy applications to investigate the effects of pharmacotherapy, surgery, and medical device therapy in various medicines from cells to soft and hard tissues are discussed, including pharmacotherapy--paclitaxel on Ishikawa and HeLa cells, telmisartan on angiotensin II, mitomycin C on strabismus surgery and eye whitening surgery, and fluoride on primary teeth--and medical device therapy--collagen cross-linking treatment for the management of progressive keratoconus, radiofrequency treatment for skin rejuvenation, physical extracorporeal shockwave therapy for healing of Achilles tendinitis, orthodontic treatment, and toothbrushing time to minimize the loss of teeth after exposure to acidic drinks.

  14. Dynamic Compensation for Two-Axis Robot Wrist Force Sensors

    Directory of Open Access Journals (Sweden)

    Junqing Ma

    2013-01-01

    Full Text Available To improve the dynamic characteristic of two-axis force sensors, a dynamic compensation method is proposed. The two-axis force sensor system is assumed to be a first-order system. The operation frequency of the system is expanded by a digital filter with backward difference network. To filter high-frequency noises, a low-pass filter is added after the dynamic compensation network. To avoid overcompensation, parameters of the proposed dynamic compensation method are defined by trial and error. Step response methods are utilized in dynamic calibration experiments. Compared to experiment data without compensation, the response time of the dynamic compensated data is reduced by 30%~40%. Experiments results demonstrate the effectiveness of our method.

  15. 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))).

  16. Substrate binding to SGLT1 investigated by single molecule force spectroscopy

    International Nuclear Information System (INIS)

    Neundlinger, I. J.

    2010-01-01

    D-glucose serves as one of the most important fuels in various organism due to its fundamental role in ATP-, protein and lipid synthesis. Thus, sustaining glucose homeostasis is a crucial issue of life as disorders can cause severe malfunctions such as glucose-galactose-malabsorbtion (GGM). Sodium-glucose co-transporter, SGLTs, especially the high affinity transporter SGLT1, play a crucial role in accumulation of glucose in the cell as they facilitate transport of the sugar into the cytoplasma across the cell membrane by a Na+-electrochemical potential. Even recently, members of the SGLT transporter family have become a therapeutic target for the treatment of hyperglycemia in type 2 diabetes. Hence, it is of particular importance to gain insights on the dynamic behavior of SGLTs during substrate binding and transport across the cell membrane on the single molecular level. In the present study, the Atomic Force Microscope (AFM) was employed to investigate the dynamic properties of the sodium-glucose co-transporter SGLT1 upon substrate binding under nearly physiological conditions. Hereto, new glucose derivatives were synthesized in order to probe the recognition efficiency of these molecules to SGLT1 embedded in the plasma membrane of living cells. A well established coupling protocol was used to covalently link (i) amino-modified D-glucose owning a conserved pyranose ring, (ii) 1-thio-β-D-glucose having a sulphur atom at C1 of the pyranose ring and (iii) the competitive inhibitor phlorizin to the AFM tip via poly(ethylene)glycol (PEG)-tether using different functional end groups and varying lengths. Binding characteristics, e.g. binding probability, interaction forces, influence of substances (glucose, phlorizin, sodium) and of molecule-linker compounds were obtained by performing single molecular recognition force spectroscopy (SMRFS) measurements. Moreover, temperature controlled radioactive binding/transport assays and SMRFS experiments yielded insights into

  17. Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions

    Energy Technology Data Exchange (ETDEWEB)

    Bradforth, S.E.

    1992-11-01

    The transition state region of a neutral bimolecular reaction may be experimentally investigated by photoelectron spectroscopy of an appropriate negative ion. The photoelectron spectrum provides information on the spectroscopy and dynamics of the short lived transition state and may be used to develop model potential energy surfaces that are semi-quantitative in this important region. The principles of bound [yields] bound negative ion photoelectron spectroscopy are illustrated by way of an example: a full analysis of the photoelectron bands of CN[sup [minus

  18. Photodissociation dynamics and spectroscopy of free radical combustion intermediates

    Energy Technology Data Exchange (ETDEWEB)

    Osborn, David Lewis [Univ. of California, Berkeley, CA (United States)

    1996-12-01

    The photodissociation spectroscopy and dynamics of free radicals is studied by the technique of fast beam photofragment translational spectroscopy. Photodetachment of internally cold, mass-selected negative ions produces a clean source of radicals, which are subsequently dissociated and detected. The photofragment yield as a function of photon energy is obtained, mapping out the dissociative and predissociative electronic states of the radical. In addition, the photodissociation dynamics, product branching ratios, and bond energies are probed at fixed photon energies by measuring the translational energy, P(ET), and angular distribution of the recoiling fragments using a time- and position-sensitive detector. Ab initio calculations are combined with dynamical and statistical models to interpret the observed data. The photodissociation of three prototypical hydrocarbon combustion intermediates forms the core of this work.

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

    Science.gov (United States)

    Nguyen, Nhan T.; Tuzcu, Ilhan

    2009-01-01

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

  20. NONLINEAR DYNAMICS OF CARBON NANOTUBES UNDER LARGE ELECTROSTATIC FORCE

    KAUST Repository

    Xu, Tiantian

    2015-06-01

    Because of the inherent nonlinearities involving the behavior of CNTs when excited by electrostatic forces, modeling and simulating their behavior is challenging. The complicated form of the electrostatic force describing the interaction of their cylindrical shape, forming upper electrodes, to lower electrodes poises serious computational challenges. This presents an obstacle against applying and using several nonlinear dynamics tools typically used to analyze the behavior of complicated nonlinear systems undergoing large motion, such as shooting, continuation, and integrity analysis techniques. This works presents an attempt to resolve this issue. We present an investigation of the nonlinear dynamics of carbon nanotubes when actuated by large electrostatic forces. We study expanding the complicated form of the electrostatic force into enough number of terms of the Taylor series. Then, we utilize this form along with an Euler-Bernoulli beam model to study for the first time the dynamic behavior of CNTs when excited by large electrostatic force. The geometric nonlinearity and the nonlinear electrostatic force are considered. An efficient reduced-order model (ROM) based on the Galerkin method is developed and utilized to simulate the static and dynamic responses of the CNTs. Several results are generated demonstrating softening and hardening behavior of the CNTs near their primary and secondary resonances. The effects of the DC and AC voltage loads on the behavior have been studied. The impacts of the initial slack level and CNT diameter are also demonstrated.

  1. Nonlinear Dynamics of Carbon Nanotubes Under Large Electrostatic Force

    KAUST Repository

    Xu, Tiantian

    2015-06-01

    Because of the inherent nonlinearities involving the behavior of CNTs when excited by electrostatic forces, modeling and simulating their behavior is challenging. The complicated form of the electrostatic force describing the interaction of their cylindrical shape, forming upper electrodes, to lower electrodes poises serious computational challenges. This presents an obstacle against applying and using several nonlinear dynamics tools typically used to analyze the behavior of complicated nonlinear systems undergoing large motion, such as shooting, continuation, and integrity analysis techniques. This works presents an attempt to resolve this issue. We present an investigation of the nonlinear dynamics of carbon nanotubes when actuated by large electrostatic forces. We study expanding the complicated form of the electrostatic force into enough number of terms of the Taylor series. Then, we utilize this form along with an Euler-Bernoulli beam model to study for the first time the dynamic behavior of CNTs when excited by large electrostatic force. The geometric nonlinearity and the nonlinear electrostatic force are considered. An efficient reduced-order model (ROM) based on the Galerkin method is developed and utilized to simulate the static and dynamic responses of the CNTs. Several results are generated demonstrating softening and hardening behavior of the CNTs near their primary and secondary resonances. The effects of the DC and AC voltage loads on the behavior have been studied. The impacts of the initial slack level and CNT diameter are also demonstrated.

  2. Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy

    Directory of Open Access Journals (Sweden)

    Minzhong Zhan

    2015-07-01

    Full Text Available The binding interaction between gallic acid (GA and lysozyme (LYS was investigated and compared by molecular dynamics (MD simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are hydrogen bonding and hydrophobic interactions. The root-mean-square deviation verified that GA and LYS bind to form a stable complex, while the root-mean-square fluctuation results showed that the stability of the GA-LYS complex at 298 K was higher than that at 310 K. The calculated free binding energies from the molecular mechanics/Poisson-Boltzmann surface area method showed that van der Waals forces and electrostatic interactions are the predominant intermolecular forces. The MD simulation was consistent with the spectral experiments. This study provides a reference for future study of the pharmacological mechanism of GA.

  3. Dynamics modeling for parallel haptic interfaces with force sensing and control.

    Science.gov (United States)

    Bernstein, Nicholas; Lawrence, Dale; Pao, Lucy

    2013-01-01

    Closed-loop force control can be used on haptic interfaces (HIs) to mitigate the effects of mechanism dynamics. A single multidimensional force-torque sensor is often employed to measure the interaction force between the haptic device and the user's hand. The parallel haptic interface at the University of Colorado (CU) instead employs smaller 1D force sensors oriented along each of the five actuating rods to build up a 5D force vector. This paper shows that a particular manipulandum/hand partition in the system dynamics is induced by the placement and type of force sensing, and discusses the implications on force and impedance control for parallel haptic interfaces. The details of a "squaring down" process are also discussed, showing how to obtain reduced degree-of-freedom models from the general six degree-of-freedom dynamics formulation.

  4. Influence of effective three-body force on the spectroscopy of 19O

    International Nuclear Information System (INIS)

    Haung, W.; Song, H.; Wang, Z.; Kuo, T.T.S.

    1983-01-01

    The purpose of the present paper is to investigate the influence of effective three-body force on the spectroscopy of 19 O. The model space was chosen as the configuration space which consists of the j-j coupling states of three valence neutrons in the s-d shell. The effective interaction including two- and three-body forces was then derived in the framework of the folded diagram method (FDM). Besides two traditional three-body terms, there is another kind of three-body force, the folded one constructed with two two-body diagrams, in FDM. The G-matrix elements of soft core Reid force were used in the numerical calculations. In the case of lacking the G-matrix elements, we adopted the matrix elements of M-3Y force as the equivalents. The results show that the influence of the effective three-body forces on the spectrum of 19 O is not of importance, but the part coming from the folded three-body term is worth noting

  5. High-throughput single-molecule force spectroscopy for membrane proteins

    Science.gov (United States)

    Bosshart, Patrick D.; Casagrande, Fabio; Frederix, Patrick L. T. M.; Ratera, Merce; Bippes, Christian A.; Müller, Daniel J.; Palacin, Manuel; Engel, Andreas; Fotiadis, Dimitrios

    2008-09-01

    Atomic force microscopy-based single-molecule force spectroscopy (SMFS) is a powerful tool for studying the mechanical properties, intermolecular and intramolecular interactions, unfolding pathways, and energy landscapes of membrane proteins. One limiting factor for the large-scale applicability of SMFS on membrane proteins is its low efficiency in data acquisition. We have developed a semi-automated high-throughput SMFS (HT-SMFS) procedure for efficient data acquisition. In addition, we present a coarse filter to efficiently extract protein unfolding events from large data sets. The HT-SMFS procedure and the coarse filter were validated using the proton pump bacteriorhodopsin (BR) from Halobacterium salinarum and the L-arginine/agmatine antiporter AdiC from the bacterium Escherichia coli. To screen for molecular interactions between AdiC and its substrates, we recorded data sets in the absence and in the presence of L-arginine, D-arginine, and agmatine. Altogether ~400 000 force-distance curves were recorded. Application of coarse filtering to this wealth of data yielded six data sets with ~200 (AdiC) and ~400 (BR) force-distance spectra in each. Importantly, the raw data for most of these data sets were acquired in one to two days, opening new perspectives for HT-SMFS applications.

  6. High-throughput single-molecule force spectroscopy for membrane proteins

    International Nuclear Information System (INIS)

    Bosshart, Patrick D; Casagrande, Fabio; Frederix, Patrick L T M; Engel, Andreas; Fotiadis, Dimitrios; Ratera, Merce; Palacin, Manuel; Bippes, Christian A; Mueller, Daniel J

    2008-01-01

    Atomic force microscopy-based single-molecule force spectroscopy (SMFS) is a powerful tool for studying the mechanical properties, intermolecular and intramolecular interactions, unfolding pathways, and energy landscapes of membrane proteins. One limiting factor for the large-scale applicability of SMFS on membrane proteins is its low efficiency in data acquisition. We have developed a semi-automated high-throughput SMFS (HT-SMFS) procedure for efficient data acquisition. In addition, we present a coarse filter to efficiently extract protein unfolding events from large data sets. The HT-SMFS procedure and the coarse filter were validated using the proton pump bacteriorhodopsin (BR) from Halobacterium salinarum and the L-arginine/agmatine antiporter AdiC from the bacterium Escherichia coli. To screen for molecular interactions between AdiC and its substrates, we recorded data sets in the absence and in the presence of L-arginine, D-arginine, and agmatine. Altogether ∼400 000 force-distance curves were recorded. Application of coarse filtering to this wealth of data yielded six data sets with ∼200 (AdiC) and ∼400 (BR) force-distance spectra in each. Importantly, the raw data for most of these data sets were acquired in one to two days, opening new perspectives for HT-SMFS applications

  7. High-throughput single-molecule force spectroscopy for membrane proteins

    Energy Technology Data Exchange (ETDEWEB)

    Bosshart, Patrick D; Casagrande, Fabio; Frederix, Patrick L T M; Engel, Andreas; Fotiadis, Dimitrios [M E Mueller Institute for Structural Biology, Biozentrum of the University of Basel, CH-4056 Basel (Switzerland); Ratera, Merce; Palacin, Manuel [Institute for Research in Biomedicine, Barcelona Science Park, Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona and Centro de Investigacion Biomedica en Red de Enfermedades Raras, E-08028 Barcelona (Spain); Bippes, Christian A; Mueller, Daniel J [BioTechnology Center, Technical University, Tatzberg 47, D-01307 Dresden (Germany)], E-mail: andreas.engel@unibas.ch, E-mail: dimitrios.fotiadis@mci.unibe.ch

    2008-09-24

    Atomic force microscopy-based single-molecule force spectroscopy (SMFS) is a powerful tool for studying the mechanical properties, intermolecular and intramolecular interactions, unfolding pathways, and energy landscapes of membrane proteins. One limiting factor for the large-scale applicability of SMFS on membrane proteins is its low efficiency in data acquisition. We have developed a semi-automated high-throughput SMFS (HT-SMFS) procedure for efficient data acquisition. In addition, we present a coarse filter to efficiently extract protein unfolding events from large data sets. The HT-SMFS procedure and the coarse filter were validated using the proton pump bacteriorhodopsin (BR) from Halobacterium salinarum and the L-arginine/agmatine antiporter AdiC from the bacterium Escherichia coli. To screen for molecular interactions between AdiC and its substrates, we recorded data sets in the absence and in the presence of L-arginine, D-arginine, and agmatine. Altogether {approx}400 000 force-distance curves were recorded. Application of coarse filtering to this wealth of data yielded six data sets with {approx}200 (AdiC) and {approx}400 (BR) force-distance spectra in each. Importantly, the raw data for most of these data sets were acquired in one to two days, opening new perspectives for HT-SMFS applications.

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

    Science.gov (United States)

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

    2015-11-01

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

  9. Laser spectroscopy and dynamics of transient species

    Energy Technology Data Exchange (ETDEWEB)

    Clouthier, D.J. [Univ. of Kentucky, Lexington (United States)

    1993-12-01

    The goal of this program is to study the vibrational and electronic spectra and excited state dynamics of a number of transient sulfur and oxygen species. A variety of supersonic jet techniques, as well as high resolution FT-IR and intracavity dye laser spectroscopy, have been applied to these studies.

  10. Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Yu H. G.; Muckerman, J.T.

    2012-05-29

    The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.

  11. Mechanical Spectroscopy: Some Applications On Structural Changes And Relaxation Dynamics In Soft Matter

    Directory of Open Access Journals (Sweden)

    Wu Xuebang

    2015-09-01

    Full Text Available The general trend in soft matter is to study systems of increasing complexity covering a wide range in time and frequency. Mechanical spectroscopy is a powerful tool for understanding the structure and relaxation dynamics of these materials over a large temperature range and frequency scale. In this work, we collect a few recent applications using low-frequency mechanical spectroscopy for elucidating the structural changes and relaxation dynamics in soft matter, largely based on the author’s group. We illustrate the potential of mechanical spectroscopy with three kinds of soft materials: colloids, polymers and granular systems. Examples include structural changes in colloids, segmental relaxations in amorphous polymers, and resonant dissipation of grain chains in three-dimensional media. The present work shows that mechanical spectroscopy has been applied as a necessary and complementary tool to study the dynamics of such complex systems.

  12. Toward the fourth dimension of membrane protein structure: insight into dynamics from spin-labeling EPR spectroscopy.

    Science.gov (United States)

    McHaourab, Hassane S; Steed, P Ryan; Kazmier, Kelli

    2011-11-09

    Trapping membrane proteins in the confines of a crystal lattice obscures dynamic modes essential for interconversion between multiple conformations in the functional cycle. Moreover, lattice forces could conspire with detergent solubilization to stabilize a minor conformer in an ensemble thus confounding mechanistic interpretation. Spin labeling in conjunction with electron paramagnetic resonance (EPR) spectroscopy offers an exquisite window into membrane protein dynamics in the native-like environment of a lipid bilayer. Systematic application of spin labeling and EPR identifies sequence-specific secondary structures, defines their topology and their packing in the tertiary fold. Long range distance measurements (60 Å-80 Å) between pairs of spin labels enable quantitative analysis of equilibrium dynamics and triggered conformational changes. This review highlights the contribution of spin labeling to bridging structure and mechanism. Efforts to develop methods for determining structures from EPR restraints and to increase sensitivity and throughput promise to expand spin labeling applications in membrane protein structural biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

  13. Dynamic response of the JT-60 vacuum vessel under the electromagnetic forces

    International Nuclear Information System (INIS)

    Takatsu, H.; Shimizu, M.; Ohta, M.

    1982-01-01

    Dynamic response analyses of the JAERI Tokamak 60 (JT-60) vacuum vessel were carried out under three kinds of saddle-like electromagnetic forces. In the analysis, the dynamic response of the bellows was obtained by dividing it into three components; the first, caused by the forced deflection due to the displacement of an adjacent rigid ring; the second, caused by inertia force; and the third, caused by a saddle-like electromagnetic force. Eigenvalue analyses showed that the 20th mode is a typical rotation mode of the rigid ring around the major radius with a natural frequency of 46.3 Hz. From the results of the dynamic response analyses, the maximum displacement response of the rigid ring was 3.1 mm and remarkable dynamic response was observed in the case of plasma disruption with a time constant of 1 ms. In cases of start-up of the plasma current and plasma disruption with a time constant of 50 ms, the rigid ring vibrates quasi-statically. It is clear that the dynamic behavior of the vacuum vessel is governed mainly by the saddle-like electromagnetic force, with a smaller effect of the inverse saddle-like electromagnetic force on the dynamic response of the vacuum vessel. (orig.)

  14. Experimental investigation of unsteady fluid dynamic forces acting on tube array

    International Nuclear Information System (INIS)

    Tanaka, Hiroki; Takahara, Shigeru; Tanaka, Mitsutoshi

    1981-01-01

    It is well-known that the cylinder bundle vibrates in cross flow. Many studies of the vibration have been made, and it has been clarified that the vibration is caused by fluid-elastic vibration coupling to neighboring cylinders. The theory given in this paper considers unsteady fluid dynamic forces to be composed of inertia forces due to added mass of fluid, damping forces of fluid which are in phase to cylinder vibrating velocity, and stiffness forces which are proportional to cylinder displacements. Furthermore, taking account of the influences of neighboring cylinder vibrations, ten kinds of unsteady fluid dynamic forces are considered to act on a cylinder in cylinder bundles. Equations of motion of cylinders were deduced and the critical velocities were calculated with the measured unsteady fluid dynamic forces. Critical velocity tests were also conducted with cylinders which were supported with elastic spars. The calculated critical velocities coincided well with the test results. (author)

  15. Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy.

    Science.gov (United States)

    Das, Priyadip; Duanias-Assaf, Tal; Reches, Meital

    2017-03-06

    The interactions between proteins or peptides and inorganic materials lead to several interesting processes. For example, combining proteins with minerals leads to the formation of composite materials with unique properties. In addition, the undesirable process of biofouling is initiated by the adsorption of biomolecules, mainly proteins, on surfaces. This organic layer is an adhesion layer for bacteria and allows them to interact with the surface. Understanding the fundamental forces that govern the interactions at the organic-inorganic interface is therefore important for many areas of research and could lead to the design of new materials for optical, mechanical and biomedical applications. This paper demonstrates a single-molecule force spectroscopy technique that utilizes an AFM to measure the adhesion force between either peptides or amino acids and well-defined inorganic surfaces. This technique involves a protocol for attaching the biomolecule to the AFM tip through a covalent flexible linker and single-molecule force spectroscopy measurements by atomic force microscope. In addition, an analysis of these measurements is included.

  16. Optical Tweezers-Based Measurements of Forces and Dynamics at Microtubule Ends.

    Science.gov (United States)

    Baclayon, Marian; Kalisch, Svenja-Marei; Hendel, Ed; Laan, Liedewij; Husson, Julien; Munteanu, E Laura; Dogterom, Marileen

    2017-01-01

    Microtubules are dynamic cytoskeletal polymers that polymerize and depolymerize while interacting with different proteins and structures within the cell. The highly regulated dynamic properties as well as the pushing and pulling forces generated by dynamic microtubule ends play important roles in processes such as in cell division. For instance, microtubule end-binding proteins are known to affect dramatically the dynamic properties of microtubules, and cortical dyneins are known to mediate pulling forces on microtubule ends. We discuss in this chapter our efforts to reconstitute these systems in vitro and mimic their interactions with structures within the cell using micro-fabricated barriers. Using an optical tweezers setup, we investigate the dynamics and forces of microtubules growing against functionalized barriers in the absence and presence of end-binding proteins and barrier-attached motor proteins. This setup allows high-speed as well as nanometer and piconewton resolution measurements on dynamic microtubules.

  17. 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.

  18. MD1405: Demonstration of forced dynamic aperture measurements at injection

    CERN Document Server

    Carlier, Felix Simon; Persson, Tobias Hakan Bjorn; Tomas Garcia, Rogelio; CERN. Geneva. ATS Department

    2017-01-01

    Accurate measurements of dynamic aperture become more important for the LHC as it advances into increasingly nonlinear regimes of operations, as well as for the High Luminosity LHC where machine nonlinearities will have a significantly larger impact. Direct dynamic aperture measurements at top energy in the LHC are challenging, and conventional single kick methods are not viable. Dynamic aperture measurements under forced oscillation of AC dipoles have been proposed as s possible alternative observable. A first demonstration of forced DA measurements at injections energy is presented.

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

    Science.gov (United States)

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

    2015-10-01

    Tapping mode atomic force microscopy (AFM) provides phase images in addition to height and amplitude images. Although the behavior of tapping mode AFM has been investigated using mathematical modeling, comprehensive understanding of the behavior of tapping mode AFM still poses a significant challenge to the AFM community, involving issues such as the correct interpretation of the phase images. In this paper, the cantilever's dynamic behavior in tapping mode AFM is studied through a three dimensional finite element method. The cantilever's dynamic displacement responses are firstly obtained via simulation under different tip-sample separations, and for different tip-sample interaction forces, such as elastic force, adhesion force, viscosity force, and the van der Waals force, which correspond to the cantilever's action upon various different representative computer-generated test samples. Simulated results show that the dynamic cantilever displacement response can be divided into three zones: a free vibration zone, a transition zone, and a contact vibration zone. Phase trajectory, phase shift, transition time, pseudo stable amplitude, and frequency changes are then analyzed from the dynamic displacement responses that are obtained. Finally, experiments are carried out on a real AFM system to support the findings of the simulations. © 2015 Wiley Periodicals, Inc.

  20. Ultrafast dynamic ellipsometry and spectroscopies of laser shocked materials

    Energy Technology Data Exchange (ETDEWEB)

    Mcgrane, Shawn David [Los Alamos National Laboratory; Bolme, Cindy B [Los Alamos National Laboratory; Whitley, Von H [Los Alamos National Laboratory; Moore, David S [Los Alamos National Laboratory

    2010-01-01

    Ultrafast ellipsometry and transient absorption spectroscopies are used to measure material dynamics under extreme conditions of temperature, pressure, and volumetric compression induced by shock wave loading with a chirped, spectrally clipped shock drive pulse.

  1. Quantifying DNA melting transitions using single-molecule force spectroscopy

    International Nuclear Information System (INIS)

    Calderon, Christopher P; Chen, W-H; Harris, Nolan C; Kiang, C-H; Lin, K-J

    2009-01-01

    We stretched a DNA molecule using an atomic force microscope (AFM) and quantified the mechanical properties associated with B and S forms of double-stranded DNA (dsDNA), molten DNA, and single-stranded DNA. We also fit overdamped diffusion models to the AFM time series and used these models to extract additional kinetic information about the system. Our analysis provides additional evidence supporting the view that S-DNA is a stable intermediate encountered during dsDNA melting by mechanical force. In addition, we demonstrated that the estimated diffusion models can detect dynamical signatures of conformational degrees of freedom not directly observed in experiments.

  2. Quantifying DNA melting transitions using single-molecule force spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Calderon, Christopher P [Department of Computational and Applied Mathematics, Rice University, Houston, TX (United States); Chen, W-H; Harris, Nolan C; Kiang, C-H [Department of Physics and Astronomy, Rice University, Houston, TX (United States); Lin, K-J [Department of Chemistry, National Chung Hsing University, Taichung, Taiwan (China)], E-mail: chkiang@rice.edu

    2009-01-21

    We stretched a DNA molecule using an atomic force microscope (AFM) and quantified the mechanical properties associated with B and S forms of double-stranded DNA (dsDNA), molten DNA, and single-stranded DNA. We also fit overdamped diffusion models to the AFM time series and used these models to extract additional kinetic information about the system. Our analysis provides additional evidence supporting the view that S-DNA is a stable intermediate encountered during dsDNA melting by mechanical force. In addition, we demonstrated that the estimated diffusion models can detect dynamical signatures of conformational degrees of freedom not directly observed in experiments.

  3. Dynamic Commitment: Wargaming Projected Forces Against the QDR Defense Strategy

    National Research Council Canada - National Science Library

    Carter, Clarence

    1997-01-01

    .... The Dynamic Commitment Wargame Series informed participants regarding the expected future demand on forces, such that Services were better able to articulate the effect of the examined force options...

  4. 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.

  5. 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

  6. An open source/real-time atomic force microscope architecture to perform customizable force spectroscopy experiments.

    Science.gov (United States)

    Materassi, Donatello; Baschieri, Paolo; Tiribilli, Bruno; Zuccheri, Giampaolo; Samorì, Bruno

    2009-08-01

    We describe the realization of an atomic force microscope architecture designed to perform customizable experiments in a flexible and automatic way. Novel technological contributions are given by the software implementation platform (RTAI-LINUX), which is free and open source, and from a functional point of view, by the implementation of hard real-time control algorithms. Some other technical solutions such as a new way to estimate the optical lever constant are described as well. The adoption of this architecture provides many degrees of freedom in the device behavior and, furthermore, allows one to obtain a flexible experimental instrument at a relatively low cost. In particular, we show how such a system has been employed to obtain measures in sophisticated single-molecule force spectroscopy experiments [Fernandez and Li, Science 303, 1674 (2004)]. Experimental results on proteins already studied using the same methodologies are provided in order to show the reliability of the measure system.

  7. Transition paths in single-molecule force spectroscopy.

    Science.gov (United States)

    Cossio, Pilar; Hummer, Gerhard; Szabo, Attila

    2018-03-28

    In a typical single-molecule force spectroscopy experiment, the ends of the molecule of interest are connected by long polymer linkers to a pair of mesoscopic beads trapped in the focus of two laser beams. At constant force load, the total extension, i.e., the end-to-end distance of the molecule plus linkers, is measured as a function of time. In the simplest systems, the measured extension fluctuates about two values characteristic of folded and unfolded states, with occasional transitions between them. We have recently shown that molecular (un)folding rates can be recovered from such trajectories, with a small linker correction, as long as the characteristic time of the bead fluctuations is shorter than the residence time in the unfolded (folded) state. Here, we show that accurate measurements of the molecular transition path times require an even faster apparatus response. Transition paths, the trajectory segments in which the molecule (un)folds, are properly resolved only if the beads fluctuate more rapidly than the end-to-end distance of the molecule. Therefore, over a wide regime, the measured rates may be meaningful but not the transition path times. Analytic expressions for the measured mean transition path times are obtained for systems diffusing anisotropically on a two-dimensional free energy surface. The transition path times depend on the properties both of the molecule and of the pulling device.

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

    Science.gov (United States)

    Wettels, Nicholas; Pletner, Baruch

    2012-04-01

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

  9. Relationships between Isometric Force-Time Characteristics and Dynamic Performance

    Directory of Open Access Journals (Sweden)

    Thomas Dos’Santos

    2017-09-01

    Full Text Available The purpose of this study was to explore the relationships between isometric mid-thigh pull (IMTP force-time characteristics (peak force and time-specific force vales (100–250 ms and dynamic performance and compare dynamic performance between stronger and weaker athletes. Forty-three athletes from different sports (rowing, soccer, bicycle motocross, and hockey performed three trials of the squat jump (SJ, countermovement jump (CMJ, and IMTP, and performed a one repetition maximum power clean (PC. Reactive strength index modified (RSImod was also calculated from the CMJ. Statistically significant large correlations between IMTP force-time characteristics and PC (ρ = 0.569–0.674, p < 0.001, and moderate correlations between IMTP force-time characteristics (excluding force at 100 ms and RSImod (ρ = 0.389–0.449, p = 0.013–0.050 were observed. Only force at 250 ms demonstrated a statistically significant moderate correlation with CMJ height (ρ = 0.346, p = 0.016 and no statistically significant associations were observed between IMTP force-time characteristics and SJ height. Stronger athletes (top 10 demonstrated statistically significantly greater CMJ heights, RSImods, and PCs (p ≤ 0.004, g = 1.32–1.89 compared to weaker (bottom 10 athletes, but no differences in SJ height were observed (p = 0.871, g = 0.06. These findings highlight that the ability to apply rapidly high levels of force in short time intervals is integral for PC, CMJ height, and reactive strength.

  10. Understanding image contrast formation in TiO.sub.2./sub. with force spectroscopy

    Czech Academy of Sciences Publication Activity Database

    Yurtsever, A.; Fernandez-Torre, D.; González, C.; Jelínek, Pavel; Pou, P.; Sugimoto, Y.; Abe, M.; Pérez, R.; Morita, S.

    2012-01-01

    Roč. 85, č. 12 (2012), "125416-1"-"125416-9" ISSN 1098-0121 R&D Projects: GA MŠk(CZ) ME10076 Institutional research plan: CEZ:AV0Z10100521 Keywords : DFT * AFM * force spectroscopy * atomic resolution Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.767, year: 2012

  11. Applications of laser-induced gratings to spectroscopy and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Rohlfing, E.A. [Sandia National Laboratories, Livermore, CA (United States)

    1993-12-01

    This program has traditionally emphasized two principal areas of research. The first is the spectroscopic characterization of large-amplitude motion on the ground-state potential surface of small, transient molecules. The second is the reactivity of carbonaceous clusters and its relevance to soot and fullerene formation in combustion. Motivated initially by the desire to find improved methods of obtaining stimulated emission pumping (SEP) spectra of transients, most of our recent work has centered on the use of laser-induced gratings or resonant four-wave mixing in free-jet expansions. These techniques show great promise for several chemical applications, including molecular spectroscopy and photodissociation dynamics. The author describes recent applications of two-color laser-induced grating spectroscopy (LIGS) to obtain background-free SEP spectra of transients and double resonance spectra of nonfluorescing species, and the use of photofragment transient gratings to probe photodissociation dynamics.

  12. Traceable calibration and demonstration of a portable dynamic force transfer standard

    Science.gov (United States)

    Vlajic, Nicholas; Chijioke, Ako

    2017-08-01

    In general, the dynamic sensitivity of a force transducer depends upon the mechanical system in which it is used. This dependence serves as motivation to develop a dynamic force transfer standard, which can be used to calibrate an application transducer in situ. In this work, we SI-traceably calibrate a hand-held force transducer, namely an impact hammer, by using a mass suspended from a thin line which is cut to produce a known dynamic force in the form of a step function. We show that this instrument is a promising candidate as a transfer standard, since its dynamic response has small variance between different users. This calibrated transfer standard is then used to calibrate a secondary force transducer in an example application setting. The combined standard uncertainty (k  =  2) in the calibration of the transfer standard was determined to be 2.1% or less, up to a bandwidth of 5 kHz. The combined standard uncertainty (k  =  2) in the performed transfer calibration was less than 4%, up to 3 kHz. An advantage of the transfer calibration framework presented here, is that the transfer standard can be used to transfer SI-traceable calibrations without the use of any SI-traceable voltage metrology instrumentation.

  13. Quantifying cellular mechanics and adhesion in renal tubular injury using single cell force spectroscopy.

    Science.gov (United States)

    Siamantouras, Eleftherios; Hills, Claire E; Squires, Paul E; Liu, Kuo-Kang

    2016-05-01

    Tubulointerstitial fibrosis represents the major underlying pathology of diabetic nephropathy where loss of cell-to-cell adhesion is a critical step. To date, research has predominantly focussed on the loss of cell surface molecular binding events that include altered protein ligation. In the current study, atomic force microscopy single cell force spectroscopy (AFM-SCFS) was used to quantify changes in cellular stiffness and cell adhesion in TGF-β1 treated kidney cells of the human proximal tubule (HK2). AFM indentation of TGF-β1 treated HK2 cells showed a significant increase (42%) in the elastic modulus (stiffness) compared to control. Fluorescence microscopy confirmed that increased cell stiffness is accompanied by reorganization of the cytoskeleton. The corresponding changes in stiffness, due to F-actin rearrangement, affected the work of detachment by changing the separation distance between two adherent cells. Overall, our novel data quantitatively demonstrate a correlation between cellular elasticity, adhesion and early morphologic/phenotypic changes associated with tubular injury. Diabetes affects many patients worldwide. One of the long term problems is diabetic nephropathy. Here, the authors utilized atomic force microscopy single cell force spectroscopy (AFM- SCFS) to study cellular stiffness and cell adhesion after TGF1 treatment in human proximal tubule kidney cells. The findings would help further understand the overall disease mechanism in diabetic patients. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Sequence-dependent unfolding kinetics of DNA hairpins studied by nanopore force spectroscopy

    International Nuclear Information System (INIS)

    Renner, Stephan; Bessonov, Andrey; Simmel, Friedrich C; Gerland, Ulrich

    2010-01-01

    Nanopore force spectroscopy is used to study the unzipping kinetics of two DNA hairpin molecules with a 12 base pair long stem containing two contiguous stretches of six GC and six AT base pairs in interchanged order. Even though the thermodynamic stabilities of the two structures are nearly the same, they differ greatly in their unzipping kinetics. When the GC segment has to be broken before the AT segment, the unfolding rate is orders of magnitude smaller than in the opposite case. We also investigated hairpins with stem regions consisting only of AT or GC base pairs. The pure AT hairpins translocate much faster than the other hairpins, whereas the pure GC hairpins translocate on similar timescales to the hairpins with only an initial GC segment. For each hairpin, nanopore force spectroscopy is performed for different loading rates and the resulting unzipping distributions are mathematically transformed to a master curve that yields the unfolding rate as a function of applied voltage. This is compared with a stochastic model of the unfolding process for the two sequences for different voltages. The results can be rationalized in terms of the different natures of the free energy landscapes for the unfolding process.

  15. Static and Dynamic Performance Simulation of Direct-Acting Force Motor Valve

    Science.gov (United States)

    Ye, Xinghai; Ding, Jianjun; Zheng, Gang; Jiang, Kunpeng; Chen, Dongdong

    2017-07-01

    This work focuses on static and dynamic characteristics of direct-acting force motor valve. First, we analyzed the structure features and operating principle of the Mitsubishi-Hitachi force motor valve (FMV) and the operating principle of its internal permanent-magnet moving-coil force motor magnetic circuit, determined the transfer function of the FMV force motor system, and established a mathematical model for the system. Secondly, we established a static performance analysis model using the AMESIM software and utilized the model in combination with experimental results to analyze the effects of electro-hydraulic servo valve structural parameters on static characteristics. Lastly, we deduced the trajectory equation of the system, established the relationship between dynamic characteristic indexes and structural parameters, and analyzed the effects of different parameter values on the dynamic characteristics of the system. This research can provide a theoretical guidance for designing and manufacturing the FMV body.

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

    Science.gov (United States)

    Güntürkün, Ulaş

    2010-07-01

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

  17. Probing static disorder in Arrhenius kinetics by single-molecule force spectroscopy.

    Science.gov (United States)

    Kuo, Tzu-Ling; Garcia-Manyes, Sergi; Li, Jingyuan; Barel, Itay; Lu, Hui; Berne, Bruce J; Urbakh, Michael; Klafter, Joseph; Fernández, Julio M

    2010-06-22

    The widely used Arrhenius equation describes the kinetics of simple two-state reactions, with the implicit assumption of a single transition state with a well-defined activation energy barrier DeltaE, as the rate-limiting step. However, it has become increasingly clear that the saddle point of the free-energy surface in most reactions is populated by ensembles of conformations, leading to nonexponential kinetics. Here we present a theory that generalizes the Arrhenius equation to include static disorder of conformational degrees of freedom as a function of an external perturbation to fully account for a diverse set of transition states. The effect of a perturbation on static disorder is best examined at the single-molecule level. Here we use force-clamp spectroscopy to study the nonexponential kinetics of single ubiquitin proteins unfolding under force. We find that the measured variance in DeltaE shows both force-dependent and independent components, where the force-dependent component scales with F(2), in excellent agreement with our theory. Our study illustrates a novel adaptation of the classical Arrhenius equation that accounts for the microscopic origins of nonexponential kinetics, which are essential in understanding the rapidly growing body of single-molecule data.

  18. PREFACE: Liquid-solid interfaces: structure and dynamics from spectroscopy and simulations Liquid-solid interfaces: structure and dynamics from spectroscopy and simulations

    Science.gov (United States)

    Gaigeot, Marie-Pierre; Sulpizi, Marialore

    2012-03-01

    /computational communities. On the experimental side, surface specific techniques, such as non-linear optical spectroscopy (sum frequency generation spectroscopy (SFG) and second harmonic generation (SHG)), surface sensitive x-ray scattering, in situ scanning tunneling microscopy (STM) and infrared reflection absorption spectroscopy provide information on layers of nanometric thickness at the interface. On the other hand, it is quite clear that the experiments require theoretical modelling in order to dissect the experimental results and to rationalize the different factors that contribute to the interfacial properties. In this respect molecular dynamics simulations are a major tool. While many successes have already been achieved with molecular dynamics simulations based on empirical force fields, first principles molecular dynamics simulations are now emerging as the other major approach where structure and reactivity are treated in a consistent way. Recent progress within the past 3-5 years on efficient treatments of basis sets and long range interactions in density functional theory (DFT) indeed extend such simulation capabilities to hundreds and thousands of atoms, thus allowing realistic models for interfaces to be tackled, maintaining first principles quality. Most of these simulations bring information on the structural organization of the solvent in the interfacial region between the solid and the liquid, but very few investigate the supplementary challenge of extracting vibrational spectroscopic fingerprints of the interface and, in particular, the direct modeling of the vibrational sum frequency generation (VSFG) non-linear spectra. The present special section reports an interesting contribution from the group of R Y Shen who pioneered VSFG optical experiments. They show how VSFG measurements can be used to unravel the behavior of interfacial water on alumina Al2O3 as a function of pH. The groups of A Hodgson and C Busse respectively provide complementary experiments based on low

  19. Semiconductor Nonlinear Dynamics Study by Broadband Terahertz Spectroscopy

    Science.gov (United States)

    Ho, I.-Chen

    Semiconductor nonlinearity in the terahertz (THz) frequency range has been attracting considerable attention due to the recent development of high-power semiconductor-based nanodevices. However, the underlying physics concerning carrier dynamics in the presence of high-field THz transients is still obscure. This thesis introduces an ultrafast, time-resolved THz pump/THz probe approach to the study of semiconductor properties in the nonlinear regime. The carrier dynamics regarding two mechanisms, intervalley scattering and impact ionization, is observed for doped InAs on a sub-picosecond time scale. In addition, polaron modulation driven by intense THz pulses is experimentally and theoretically investigated. The observed polaron dynamics verifies the interaction between energetic electrons and a phonon field. In contrast to previous work which reports optical phonon responses, acoustic phonon modulations are addressed in this study. A further understanding of the intense field interacting with solid materials will accelerate the development of semiconductor devices. This thesis starts with the design and performance of a table-top THz spectrometer which has the advantages of ultra-broad bandwidth (one order higher bandwidth compared to a conventional ZnTe sensor) and high electric field strength (>100 kV/cm). Unlike the conventional THz time-domain spectroscopy, the spectrometer integrates a novel THz air-biased-coherent-detection (THz-ABCD) technique and utilizes selected gases as THz emitters and sensors. In comparison with commonly used electro-optic (EO) crystals or photoconductive (PC) dipole antennas, the gases have the benefits of no phonon absorption as existing in EO crystals and no carrier life time limitation as observed in PC dipole antennas. The newly development THz-ABCD spectrometer with a strong THz field strength capability provides a platform for various research topics especially on the nonlinear carrier dynamics of semiconductors. Two mechanisms

  20. Mobile Charge Generation Dynamics in P3HT:PCBM Observed by Time-Resolved Terahertz Spectroscopy

    DEFF Research Database (Denmark)

    Cooke, D. G.; Krebs, Frederik C; Jepsen, Peter Uhd

    2012-01-01

    Ultra-broadband time-resolved terahertz spectroscopy is used to examine the sub-ps conductivity dynamics of a conjugated polymer bulk heterojunction film P3HT:PCBM. We directly observe mobile charge generation dynamics on a sub-100 fs time scale.......Ultra-broadband time-resolved terahertz spectroscopy is used to examine the sub-ps conductivity dynamics of a conjugated polymer bulk heterojunction film P3HT:PCBM. We directly observe mobile charge generation dynamics on a sub-100 fs time scale....

  1. Mobile charge generation dynamics in P3HT: PCBM observed by time-resolved terahertz spectroscopy

    DEFF Research Database (Denmark)

    Cooke, D. G.; Krebs, Frederik C; Jepsen, Peter Uhd

    2012-01-01

    Ultra-broadband time-resolved terahertz spectroscopy is used to examine the sub-ps conductivity dynamics of a conjugated polymer bulk heterojunction film P3HT:PCBM. We directly observe mobile charge generation dynamics on a sub-100 fs time scale.......Ultra-broadband time-resolved terahertz spectroscopy is used to examine the sub-ps conductivity dynamics of a conjugated polymer bulk heterojunction film P3HT:PCBM. We directly observe mobile charge generation dynamics on a sub-100 fs time scale....

  2. Dynamical interactions between solute and solvent studied by nonlinear infrared spectroscopy

    International Nuclear Information System (INIS)

    Ohta, K.; Tominaga, K.

    2006-01-01

    Interactions between solute and solvent play an important role in chemical reaction dynamics and in many relaxation processes in condensed phases. Recently third-order nonlinear infrared (IR) spectroscopy has shown to be useful to investigate solute-solvent interaction and dynamics of the vibrational transition. These studies provide detailed information on the energy relaxation of the vibrationally excited state, and the time scale and the magnitude of the time correlation functions of the vibrational frequency fluctuations. In this work we have studied vibrational energy relaxation (VER) of solutions and molecular complexes by nonlinear IR spectroscopy, especially IR pump-probe method, to understand the microscopic interactions in liquids. (authors)

  3. Measurement of dynamic bite force during mastication.

    Science.gov (United States)

    Shimada, A; Yamabe, Y; Torisu, T; Baad-Hansen, L; Murata, H; Svensson, P

    2012-05-01

    Efficient mastication of different types and size of food depends on fast integration of sensory information from mechanoreceptors and central control mechanisms of jaw movements and applied bite force. The neural basis underlying mastication has been studied for decades but little progress in understanding the dynamics of bite force has been made mainly due to technical limitations of bite force recorders. The aims of this study were to develop a new intraoral bite force recorder which would allow the study of natural mastication without an increase in the occlusal vertical dimension and subsequently to analyze the relation between electromyographic (EMG) activity of jaw-closing muscles, jaw movements and bite force during mastication of five different types of food. Customized force recorders based on strain gauge sensors were fitted to the upper and lower molar teeth on the preferred chewing side in fourteen healthy and dentate subjects (21-39 years), and recordings were carried out during voluntary mastication of five different kinds of food. Intraoral force recordings were successively obtained from all subjects. anova showed that impulse of bite force as well as integrated EMG was significantly influenced by food (Pmastication with direct implications for oral rehabilitation. We also propose that the control of bite force during mastication is achieved by anticipatory adjustment and encoding of bolus characteristics. © 2012 Blackwell Publishing Ltd.

  4. High resolution neutron spectroscopy - a tool for the investigation of dynamics of polymers and soft matter

    International Nuclear Information System (INIS)

    Monkenbusch, M.; Richter, D.

    2007-01-01

    Neutron scattering, with the ability to vary the contrast of molecular items by hydrogen/deuterium exchanges, is an invaluable tool for soft matter research. Besides the structural information on the mesoscopic scale that is obtained by diffraction methods like small angle neutron scattering, the slow dynamics of molecular motion on mesoscopic scale is accessible by high resolution neutron spectroscopy. The basic features of neutron backscattering spectroscopy, and in particular neutron spin-echo spectroscopy, are presented, in combination with illustrations of results from polymer melt dynamics to protein dynamics which are obtained by these techniques. (authors)

  5. Handling of impact forces in inverse dynamics

    NARCIS (Netherlands)

    Bisseling, Rob W.; Hof, At L.

    2006-01-01

    In the standard inverse dynamic method, joint moments are assessed from ground reaction force data and position data, where segmental accelerations are calculated by numerical differentiation of position data after low-pass filtering. This method falls short in analyzing the impact phase, e.g.

  6. Ground Reaction Forces Generated During Rhythmical Squats as a Dynamic Loads of the Structure

    Science.gov (United States)

    Pantak, Marek

    2017-10-01

    Dynamic forces generated by moving persons can lead to excessive vibration of the long span, slender and lightweight structure such as floors, stairs, stadium stands and footbridges. These dynamic forces are generated during walking, running, jumping and rhythmical body swaying in vertical or horizontal direction etc. In the paper the mathematical models of the Ground Reaction Forces (GRFs) generated during squats have been presented. Elaborated models was compared to the GRFs measured during laboratory tests carried out by author in wide range of frequency using force platform. Moreover, the GRFs models were evaluated during dynamic numerical analyses and dynamic field tests of the exemplary structure (steel footbridge).

  7. Analysis of Dynamic Inertia Forces at Main Bearing of Ship Reciprocating Engines

    Directory of Open Access Journals (Sweden)

    F. Louhenapessy Louhenapessy,

    2010-11-01

    Full Text Available During operation, a ship reciprocating engine will vibrate due to the force resulting from the cycle movement of the dynamic components. Soon or later, the vibration will cause wear of engine components. Therefore, the cause of vibration should be early identified so that the propagation of wear can be anticipated. The study modeled the ship reciprocating engine as a two stroke engine, and analyzed one of the causes of the engine vibration, i.e. the force acting on main bearing, using a numerical simulation. An experimental study was also carried out for measuring the acceleration of vibration response due to the numerical dynamic inertia force. The results showed that the dynamic inertia force acting on the main bearing is the main cause of the vibration of engine.

  8. Two-dimensional optical correlation spectroscopy applied to liquid/glass dynamics

    OpenAIRE

    Lazonder, Kees; Pshenichnikov, Maxim S.; Wiersma, Douwe A.; Corkum, Paul; Jonas, David M.; Miller, R.J. Dwayne.; Weiner, Andrew M.

    2007-01-01

    Correlation spectroscopy was used to study the effects of temperature and phase changes on liquid and glass solvent dynamics. By assessing the eccentricity of the elliptic shape of a 2D optical correlation spectrum the value of the underlying frequency-frequency correlation function can be retrieved through a very simple relationship. This method yielded both intuitive clues and a quantitative measure of the dynamics of the system.

  9. Quantifying bacterial adhesion on antifouling polymer brushes via single-cell force spectroscopy

    Czech Academy of Sciences Publication Activity Database

    Rodriguez-Emmenegger, Cesar; Janel, S.; de los Santos Pereira, Andres; Bruns, M.; Lafont, F.

    2015-01-01

    Roč. 6, č. 31 (2015), s. 5740-5751 ISSN 1759-9954 R&D Projects: GA ČR(CZ) GJ15-09368Y; GA MŠk(CZ) ED1.1.00/02.0109 Grant - others:OPPK(XE) CZ.2.16/3.1.00/21545 Program:OPPK Institutional support: RVO:61389013 Keywords : antifouling polymer brushes * single-cell force spectroscopy * bacterial adhesion Subject RIV: BO - Biophysics Impact factor: 5.687, year: 2015

  10. AFM-based force spectroscopy measurements of mature amyloid fibrils of the peptide glucagon

    DEFF Research Database (Denmark)

    Dong, M. D.; Hovgaard, M. B.; Mamdouh, W.

    2008-01-01

    We report on the mechanical characterization of individual mature amyloid fibrils by atomic force microscopy (AFM) and AFM-based single-molecule force spectroscopy (SMFS). These self-assembling materials, formed from the 29-residue amphiphatic peptide hormone glucagon, were found to display...... a reversible elastic behaviour. Based on AFM morphology and SMFS studies, we suggest that the observed elasticity is due to a force-induced conformational transition which is reversible due to the beta-helical conformation of protofibrils, allowing a high degree of extension. The elastic properties...... of such mature fibrils contribute to their high stability, suggesting that the internal hydrophobic interactions of amyloid fibrils are likely to be of fundamental importance in the assembly of amyloid fibrils and therefore for the understanding of the progression of their associated pathogenic disorders...

  11. A Force Method Model for Dynamic Analysis of Flat-Sag Cable Structures

    Directory of Open Access Journals (Sweden)

    Xing Ma

    2009-01-01

    Full Text Available A new force method is proposed for analysing the dynamic behaviour of oscillating cables with small sags. The accepted dynamic model of such cables reduces to a partial differential equation (the equation of motion and an integral equation (the compatibility equation. In the paper, D’Alembert’s travelling wave solution is applied to the partial differential equation (PDE. Substituting the solution into the compatibility and boundary conditions, the governing equation is obtained in terms of the dynamic tension increment. This equation has been named the force method dynamic equation (FMDE. In this way the infinite-degree-of-freedom dynamic system is effectively simplified to a system with only one unknown. Explicit solutions for both single-span and multi-span cable systems are derived. The natural frequencies obtained from the FMDE are shown to be identical to those deduced using the conventional displacement method (DM. Nonlinear governing equations are developed by considering the effect of quadratic and cubic displacement terms. Finally, two examples are presented to illustrate the accuracy of the proposed force method for single and multi-span cable systems subjected to harmonic forces.

  12. Manipulating Si(100) at 5 K using qPlus frequency modulated atomic force microscopy: Role of defects and dynamics in the mechanical switching of atoms

    Science.gov (United States)

    Sweetman, A.; Jarvis, S.; Danza, R.; Bamidele, J.; Kantorovich, L.; Moriarty, P.

    2011-08-01

    We use small-amplitude qPlus frequency modulated atomic force microscopy (FM-AFM), at 5 K, to investigate the atomic-scale mechanical stability of the Si(100) surface. By operating at zero applied bias the effect of tunneling electrons is eliminated, demonstrating that surface manipulation can be performed by solely mechanical means. Striking differences in surface response are observed between different regions of the surface, most likely due to variations in strain associated with the presence of surface defects. We investigate the variation in local energy surface by ab initio simulation, and comment on the dynamics observed during force spectroscopy.

  13. Does dynamic stability govern propulsive force generation in human walking?

    Science.gov (United States)

    Browne, Michael G; Franz, Jason R

    2017-11-01

    Before succumbing to slower speeds, older adults may walk with a diminished push-off to prioritize stability over mobility. However, direct evidence for trade-offs between push-off intensity and balance control in human walking, independent of changes in speed, has remained elusive. As a critical first step, we conducted two experiments to investigate: (i) the independent effects of walking speed and propulsive force ( F P ) generation on dynamic stability in young adults, and (ii) the extent to which young adults prioritize dynamic stability in selecting their preferred combination of walking speed and F P generation. Subjects walked on a force-measuring treadmill across a range of speeds as well as at constant speeds while modulating their F P according to a visual biofeedback paradigm based on real-time force measurements. In contrast to improvements when walking slower, walking with a diminished push-off worsened dynamic stability by up to 32%. Rather, we find that young adults adopt an F P at their preferred walking speed that maximizes dynamic stability. One implication of these findings is that the onset of a diminished push-off in old age may independently contribute to poorer balance control and precipitate slower walking speeds.

  14. Going Vertical To Improve the Accuracy of Atomic Force Microscopy Based Single-Molecule Force Spectroscopy.

    Science.gov (United States)

    Walder, Robert; Van Patten, William J; Adhikari, Ayush; Perkins, Thomas T

    2018-01-23

    Single-molecule force spectroscopy (SMFS) is a powerful technique to characterize the energy landscape of individual proteins, the mechanical properties of nucleic acids, and the strength of receptor-ligand interactions. Atomic force microscopy (AFM)-based SMFS benefits from ongoing progress in improving the precision and stability of cantilevers and the AFM itself. Underappreciated is that the accuracy of such AFM studies remains hindered by inadvertently stretching molecules at an angle while measuring only the vertical component of the force and extension, degrading both measurements. This inaccuracy is particularly problematic in AFM studies using double-stranded DNA and RNA due to their large persistence length (p ≈ 50 nm), often limiting such studies to other SMFS platforms (e.g., custom-built optical and magnetic tweezers). Here, we developed an automated algorithm that aligns the AFM tip above the DNA's attachment point to a coverslip. Importantly, this algorithm was performed at low force (10-20 pN) and relatively fast (15-25 s), preserving the connection between the tip and the target molecule. Our data revealed large uncorrected lateral offsets for 100 and 650 nm DNA molecules [24 ± 18 nm (mean ± standard deviation) and 180 ± 110 nm, respectively]. Correcting this offset yielded a 3-fold improvement in accuracy and precision when characterizing DNA's overstretching transition. We also demonstrated high throughput by acquiring 88 geometrically corrected force-extension curves of a single individual 100 nm DNA molecule in ∼40 min and versatility by aligning polyprotein- and PEG-based protein-ligand assays. Importantly, our software-based algorithm was implemented on a commercial AFM, so it can be broadly adopted. More generally, this work illustrates how to enhance AFM-based SMFS by developing more sophisticated data-acquisition protocols.

  15. 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.

  16. Valence force fields and the lattice dynamics of beryllium oxide

    International Nuclear Information System (INIS)

    Ramani, R.; Mani, K.K.; Singh, R.P.

    1976-01-01

    The lattice dynamics of beryllium oxide have been studied using a rigid-ion model, with short-range forces represented by a valence force field. Various existing calculations on group-IV elements using such a field have been examined as a prelude to transference of force constants from diamond to beryllium oxide. The effects of ionicity on the force constants have been included in the form of scale factors. It is shown that no satisfactory fit to the long-wavelength data on BeO can be found with transferred force constants. However, adequate least-squares fits can be found both with four- and six-parameter valence force fields, the discrepancy with experiment being large only for one optical mode at the Brillouin-zone center. Dispersion curves along Δ and Σ are presented and are in fair agreement with experiment, deviations arising essentially from the quality of the fit to the long-wavelength data. The bond-bending interactions are found to play a significant role and arguments have been presented to show that the inclusion of further angle-angle interactions would yield a very satisfactory picture of the dynamics

  17. 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

  18. Dynamics of cell area and force during spreading.

    Science.gov (United States)

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

    2014-12-16

    Experiments on human pulmonary artery endothelial cells are presented to show that cell area and the force exerted on a substrate increase simultaneously, but with different rates during spreading; rapid-force increase systematically occurred several minutes past initial spreading. We examine this theoretically and present three complementary mechanisms that may accompany the development of lamellar stress during spreading and underlie the observed behavior. These include: 1), the dynamics of cytoskeleton assembly at the cell basis; 2), the strengthening of acto-myosin forces in response to the generated lamellar stresses; and 3), the passive strain-stiffening of the cytoskeleton. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  19. Membrane Disruption Mechanism of a Prion Peptide (106-126) Investigated by Atomic Force Microscopy, Raman and Electron Paramagnetic Resonance Spectroscopy.

    Science.gov (United States)

    Pan, Jianjun; Sahoo, Prasana K; Dalzini, Annalisa; Hayati, Zahra; Aryal, Chinta M; Teng, Peng; Cai, Jianfeng; Rodriguez Gutierrez, Humberto; Song, Likai

    2017-05-18

    A fragment of the human prion protein spanning residues 106-126 (PrP106-126) recapitulates many essential properties of the disease-causing protein such as amyloidogenicity and cytotoxicity. PrP106-126 has an amphipathic characteristic that resembles many antimicrobial peptides (AMPs). Therefore, the toxic effect of PrP106-126 could arise from a direct association of monomeric peptides with the membrane matrix. Several experimental approaches are employed to scrutinize the impacts of monomeric PrP106-126 on model lipid membranes. Porous defects in planar bilayers are observed by using solution atomic force microscopy. Adding cholesterol does not impede defect formation. A force spectroscopy experiment shows that PrP106-126 reduces Young's modulus of planar lipid bilayers. We use Raman microspectroscopy to study the effect of PrP106-126 on lipid atomic vibrational dynamics. For phosphatidylcholine lipids, PrP106-126 disorders the intrachain conformation, while the interchain interaction is not altered; for phosphatidylethanolamine lipids, PrP106-126 increases the interchain interaction, while the intrachain conformational order remains similar. We explain the observed differences by considering different modes of peptide insertion. Finally, electron paramagnetic resonance spectroscopy shows that PrP106-126 progressively decreases the orientational order of lipid acyl chains in magnetically aligned bicelles. Together, our experimental data support the proposition that monomeric PrP106-126 can disrupt lipid membranes by using similar mechanisms found in AMPs.

  20. Dynamic steering beams for efficient force measurement in optical manipulation

    Institute of Scientific and Technical Information of China (English)

    Xiaocong Yuan; Yuquan Zhang; Rui Cao; Xing Zhao; Jing Bu; Siwei Zhu

    2011-01-01

    @@ An efficient and inexpensive method that uses a glass plate mounted onto a motorized rotating stage as a beam-steering device for the generation of dynamic optical traps is reported.Force analysis reveals that there are drag and trapping forces imposed on the bead in the opposite directions, respectively, in a viscous medium.The trapped bead will be rotated following the beam's motion before it reaches the critical escape velocity when the drag force is equal to the optical trapping force.The equilibrium condition facilitates the experimental measurement of the drag force with potential extensions to the determination of the viscosity of the medium or the refractive index of the bead.The proposed technique can easily be integrated into conventional optical microscopic systems with minimum modifications.%An efficient and inexpensive method that uses a glass plate mounted onto a motorized rotating stage as a beam-steering device for the generation of dynamic optical traps is reported. Force analysis reveals that there are drag and trapping forces imposed on the bead in the opposite directions, respectively, in a viscous medium. The trapped bead will be rotated following the beam's motion before it reaches the critical escape velocity when the drag force is equal to the optical trapping force. The equilibrium condition facilitates the experimental measurement of the drag force with potential extensions to the determination of the viscosity of the medium or the refractive index of the bead. The proposed technique can easily be integrated into conventional optical microscopic systems with minimum modifications.

  1. A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

    Directory of Open Access Journals (Sweden)

    Mingyuan Xu

    2018-05-01

    Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

  2. Investigating the binding behaviour of two avidin-based testosterone binders using molecular recognition force spectroscopy.

    Science.gov (United States)

    Rangl, Martina; Leitner, Michael; Riihimäki, Tiina; Lehtonen, Soili; Hytönen, Vesa P; Gruber, Hermann J; Kulomaa, Markku; Hinterdorfer, Peter; Ebner, Andreas

    2014-02-01

    Molecular recognition force spectroscopy, a biosensing atomic force microscopy technique allows to characterise the dissociation of ligand-receptor complexes at the molecular level. Here, we used molecular recognition force spectroscopy to study the binding capability of recently developed testosterone binders. The two avidin-based proteins called sbAvd-1 and sbAvd-2 are expected to bind both testosterone and biotin but differ in their binding behaviour towards these ligands. To explore the ligand binding and dissociation energy landscape of these proteins, we tethered biotin or testosterone to the atomic force microscopy probe while the testosterone-binding protein was immobilized on the surface. Repeated formation and rupture of the ligand-receptor complex at different pulling velocities allowed determination of the loading rate dependence of the complex-rupturing force. In this way, we obtained the molecular dissociation rate (k(off)) and energy landscape distances (x(β)) of the four possible complexes: sbAvd-1-biotin, sbAvd-1-testosterone, sbAvd-2-biotin and sbAvd-2-testosterone. It was found that the kinetic off-rates for both proteins and both ligands are similar. In contrast, the x(β) values, as well as the probability of complex formations, varied considerably. In addition, competitive binding experiments with biotin and testosterone in solution differ significantly for the two testosterone-binding proteins, implying a decreased cross-reactivity of sbAvd-2. Unravelling the binding behaviour of the investigated testosterone-binding proteins is expected to improve their usability for possible sensing applications. Copyright © 2014 John Wiley & Sons, Ltd.

  3. Collision avoidance for multiple Lagrangian dynamical systems with gyroscopic forces

    Directory of Open Access Journals (Sweden)

    Lorenzo Sabattini

    2017-01-01

    Full Text Available This article introduces a novel methodology for dealing with collision avoidance for groups of mobile robots. In particular, full dynamics are considered, since each robot is modeled as a Lagrangian dynamical system moving in a three-dimensional environment. Gyroscopic forces are utilized for defining the collision avoidance control strategy: This kind of forces leads to avoiding collisions, without interfering with the convergence properties of the multi-robot system’s desired control law. Collision avoidance introduces, in fact, a perturbation on the nominal behavior of the system: We define a method for choosing the direction of the gyroscopic force in an optimal manner, in such a way that perturbation is minimized. Collision avoidance and convergence properties are analytically demonstrated, and simulation results are provided for validation purpose.

  4. Approximate photochemical dynamics of azobenzene with reactive force fields

    Science.gov (United States)

    Li, Yan; Hartke, Bernd

    2013-12-01

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

  5. Elastic Properties of Nucleic Acids by Single-Molecule Force Spectroscopy.

    Science.gov (United States)

    Camunas-Soler, Joan; Ribezzi-Crivellari, Marco; Ritort, Felix

    2016-07-05

    We review the current knowledge on the use of single-molecule force spectroscopy techniques to extrapolate the elastic properties of nucleic acids. We emphasize the lesser-known elastic properties of single-stranded DNA. We discuss the importance of accurately determining the elastic response in pulling experiments, and we review the simplest models used to rationalize the experimental data as well as the experimental approaches used to pull single-stranded DNA. Applications used to investigate DNA conformational transitions and secondary structure formation are also highlighted. Finally, we provide an overview of the effects of salt and temperature and briefly discuss the effects of contour length and sequence dependence.

  6. Resonance Ionization Mass Spectrometry (RIMS): applications in spectroscopy and chemical dynamics

    International Nuclear Information System (INIS)

    Naik, P.D.; Kumar, Awadhesh; Upadhyaya, Hari; Bajaj, P.N.

    2009-01-01

    Resonance ionization is a photophysical process wherein electromagnetic radiation is used to ionize atoms, molecules, transient species, etc., by exciting them through their quantum states. The number of photons required to ionize depends on the species being investigated and energy of the photon. Once a charged particle is produced, it is easy to detect it with high efficiency. With the advent of narrow band high power pulsed and cw tunable dye lasers, it has blossomed into a powerful spectroscopic and analytical technique, commonly known as resonance ionization spectroscopy (RIS)/resonance enhanced multiphoton ionization (REMPI). The alliance of resonance ionization with mass spectrometry has grown into a still more powerful technique, known as resonance ionization mass spectrometry (RIMS), which has made significant contributions in a variety of frontier areas of research and development, such as spectroscopy, chemical dynamics, analytical chemistry, cluster science, surface science, radiochemistry, nuclear physics, biology, environmental science, material science, etc. In this article, we shall describe the application of resonance ionization mass spectrometry to spectroscopy of uranium and chemical dynamics of polyatomic molecules

  7. AFM-based force spectroscopy on polystyrene brushes: effect of brush thickness on protein adsorption.

    Science.gov (United States)

    Hentschel, Carsten; Wagner, Hendrik; Smiatek, Jens; Heuer, Andreas; Fuchs, Harald; Zhang, Xi; Studer, Armido; Chi, Lifeng

    2013-02-12

    Herein we present a study on nonspecific binding of proteins at highly dense packed hydrophobic polystyrene brushes. In this context, an atomic force microscopy tip was functionalized with concanavalin A to perform single-molecule force spectroscopy measurements on polystyrene brushes with thicknesses of 10 and 60 nm, respectively. Polystyrene brushes with thickness of 10 nm show an almost two times stronger protein adsorption than brushes with a thickness of 60 nm: 72 pN for the thinner and 38 pN for the thicker layer, which is in qualitative agreement with protein adsorption studies conducted macroscopically by fluorescence microscopy.

  8. Photodissociation spectroscopy and dynamics of free radicals, clusters, and ions

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Hyeon [Univ. of California, Berkeley, CA (United States)

    1999-12-01

    The photodissociation spectroscopy and dynamics of free radicals and ions is studied to characterize the dissociative electronic states in these species. To accomplish this, a special method of radical production, based on the photodetachment of the corresponding negative ion, has been combined with the technique of fast beam photofragment translational spectroscopy. The photofragment yield as a function of photon energy is obtained, mapping out the dissociative and predissociative electronic states. Branching ratios to various product channels, the translational energy distributions of the fragments, and bond dissociation energies are then determined at selected photon energies. The detailed picture of photodissociation dynamics is provided with the aid of ab initio calculations and a statistical model to interpret the observed data. Important reaction intermediates in combustion reactions have been studied: CCO, C2H5O, and linear Cn (n = 4--6).

  9. Dynamical signatures of isometric force control as a function of age, expertise, and task constraints.

    Science.gov (United States)

    Vieluf, Solveig; Sleimen-Malkoun, Rita; Voelcker-Rehage, Claudia; Jirsa, Viktor; Reuter, Eva-Maria; Godde, Ben; Temprado, Jean-Jacques; Huys, Raoul

    2017-07-01

    From the conceptual and methodological framework of the dynamical systems approach, force control results from complex interactions of various subsystems yielding observable behavioral fluctuations, which comprise both deterministic (predictable) and stochastic (noise-like) dynamical components. Here, we investigated these components contributing to the observed variability in force control in groups of participants differing in age and expertise level. To this aim, young (18-25 yr) as well as late middle-aged (55-65 yr) novices and experts (precision mechanics) performed a force maintenance and a force modulation task. Results showed that whereas the amplitude of force variability did not differ across groups in the maintenance tasks, in the modulation task it was higher for late middle-aged novices than for experts and higher for both these groups than for young participants. Within both tasks and for all groups, stochastic fluctuations were lowest where the deterministic influence was smallest. However, although all groups showed similar dynamics underlying force control in the maintenance task, a group effect was found for deterministic and stochastic fluctuations in the modulation task. The latter findings imply that both components were involved in the observed group differences in the variability of force fluctuations in the modulation task. These findings suggest that between groups the general characteristics of the dynamics do not differ in either task and that force control is more affected by age than by expertise. However, expertise seems to counteract some of the age effects. NEW & NOTEWORTHY Stochastic and deterministic dynamical components contribute to force production. Dynamical signatures differ between force maintenance and cyclic force modulation tasks but hardly between age and expertise groups. Differences in both stochastic and deterministic components are associated with group differences in behavioral variability, and observed behavioral

  10. Optimizing 1-μs-Resolution Single-Molecule Force Spectroscopy on a Commercial Atomic Force Microscope.

    Science.gov (United States)

    Edwards, Devin T; Faulk, Jaevyn K; Sanders, Aric W; Bull, Matthew S; Walder, Robert; LeBlanc, Marc-Andre; Sousa, Marcelo C; Perkins, Thomas T

    2015-10-14

    Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is widely used to mechanically measure the folding and unfolding of proteins. However, the temporal resolution of a standard commercial cantilever is 50-1000 μs, masking rapid transitions and short-lived intermediates. Recently, SMFS with 0.7-μs temporal resolution was achieved using an ultrashort (L = 9 μm) cantilever on a custom-built, high-speed AFM. By micromachining such cantilevers with a focused ion beam, we optimized them for SMFS rather than tapping-mode imaging. To enhance usability and throughput, we detected the modified cantilevers on a commercial AFM retrofitted with a detection laser system featuring a 3-μm circular spot size. Moreover, individual cantilevers were reused over multiple days. The improved capabilities of the modified cantilevers for SMFS were showcased by unfolding a polyprotein, a popular biophysical assay. Specifically, these cantilevers maintained a 1-μs response time while eliminating cantilever ringing (Q ≅ 0.5). We therefore expect such cantilevers, along with the instrumentational improvements to detect them on a commercial AFM, to accelerate high-precision AFM-based SMFS studies.

  11. A novel aptasensor based on single-molecule force spectroscopy for highly sensitive detection of mercury ions.

    Science.gov (United States)

    Li, Qing; Michaelis, Monika; Wei, Gang; Colombi Ciacchi, Lucio

    2015-08-07

    We have developed a novel aptasensor based on single-molecule force spectroscopy (SMFS) capable of detecting mercury ions (Hg(2+)) with sub-nM sensitivity. The single-strand (ss) DNA aptamer used in this work is rich in thymine (T) and readily forms T-Hg(2+)-T complexes in the presence of Hg(2+). The aptamer was conjugated to an atomic force microscope (AFM) probe, and the adhesion force between the probe and a flat graphite surface was measured by single-molecule force spectroscopy (SMFS). The presence of Hg(2+) ions above a concentration threshold corresponding to the affinity constant of the ions for the aptamer (about 5 × 10(9) M(-1)) could be easily detected by a change of the measured adhesion force. With our chosen aptamer, we could reach an Hg(2+) detection limit of 100 pM, which is well below the maximum allowable level of Hg(2+) in drinking water. In addition, this aptasensor presents a very high selectivity for Hg(2+) over other metal cations, such as K(+), Ca(2+), Zn(2+), Fe(2+), and Cd(2+). Furthermore, the effects of the ionic strength and loading rate on the Hg(2+) detection were evaluated. Its simplicity, reproducibility, high selectivity and sensitivity make our SMFS-based aptasensor advantageous with respect to other current Hg(2+) sensing methods. It is expected that our strategy can be exploited for monitoring the pollution of water environments and the safety of potentially contaminated food.

  12. Accuracy of dynamical-decoupling-based spectroscopy of Gaussian noise

    Science.gov (United States)

    Szańkowski, Piotr; Cywiński, Łukasz

    2018-03-01

    The fundamental assumption of dynamical-decoupling-based noise spectroscopy is that the coherence decay rate of qubit (or qubits) driven with a sequence of many pulses, is well approximated by the environmental noise spectrum spanned on frequency comb defined by the sequence. Here we investigate the precise conditions under which this commonly used spectroscopic approach is quantitatively correct. To this end we focus on two representative examples of spectral densities: the long-tailed Lorentzian, and finite-ranged Gaussian—both expected to be encountered when using the qubit for nanoscale nuclear resonance imaging. We have found that, in contrast to Lorentz spectrum, for which the corrections to the standard spectroscopic formulas can easily be made negligible, the spectra with finite range are more challenging to reconstruct accurately. For Gaussian line shape of environmental spectral density, direct application of the standard dynamical-decoupling-based spectroscopy leads to erroneous attribution of long-tail behavior to the reconstructed spectrum. Fortunately, artifacts such as this, can be completely avoided with the simple extension to standard reconstruction method.

  13. Antigen-antibody biorecognition events as discriminated by noise analysis of force spectroscopy curves.

    Science.gov (United States)

    Bizzarri, Anna Rita; Cannistraro, Salvatore

    2014-08-22

    Atomic force spectroscopy is able to extract kinetic and thermodynamic parameters of biomolecular complexes provided that the registered unbinding force curves could be reliably attributed to the rupture of the specific complex interactions. To this aim, a commonly used strategy is based on the analysis of the stretching features of polymeric linkers which are suitably introduced in the biomolecule-substrate immobilization procedure. Alternatively, we present a method to select force curves corresponding to specific biorecognition events, which relies on a careful analysis of the force fluctuations of the biomolecule-functionalized cantilever tip during its approach to the partner molecules immobilized on a substrate. In the low frequency region, a characteristic 1/f (α) noise with α equal to one (flickering noise) is found to replace white noise in the cantilever fluctuation power spectrum when, and only when, a specific biorecognition process between the partners occurs. The method, which has been validated on a well-characterized antigen-antibody complex, represents a fast, yet reliable alternative to the use of linkers which may involve additional surface chemistry and reproducibility concerns.

  14. 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.

  15. 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

  16. On the contribution of circumferential resonance modes in acoustic radiation force experienced by cylindrical shells

    Science.gov (United States)

    Rajabi, Majid; Behzad, Mehdi

    2014-10-01

    A body insonified by a constant (time-varying) intensity sound field is known to experience a steady (oscillatory) force that is called the steady-state (dynamic) acoustic radiation force. Using the classical resonance scattering theorem (RST) which suggests the scattered field as a superposition of a resonance field and a background (non-resonance) component, we show that the radiation force acting on a cylindrical shell may be synthesized as a composition of three components: background part, resonance part and their interaction. The background component reveals the pure geometrical reflection effects and illustrates a regular behavior with respect to frequency, while the others demonstrate a singular behavior near the resonance frequencies. The results illustrate that the resonance effects associated to partial waves can be isolated by the subtraction of the background component from the total (steady-state or dynamic) radiation force function (i.e., residue component). In the case of steady-state radiation force, the components are exerted on the body as static forces. For the case of oscillatory amplitude excitation, the components are exerted at the modulation frequency with frequency-dependant phase shifts. The results demonstrate the dominant contribution of the non-resonance component of dynamic radiation force at high frequencies with respect to the residue component, which offers the potential application of ultrasound stimulated vibro-acoustic spectroscopy technique in low frequency resonance spectroscopy purposes. Furthermore, the proposed formulation may be useful essentially due to its intrinsic value in physical acoustics. In addition, it may unveil the contribution of resonance modes in the dynamic radiation force experienced by the cylindrical objects and its underlying physics.

  17. Dynamics of force and muscle stimulation in human vertical jumping

    NARCIS (Netherlands)

    Bobbert, M.F.; van Zandwijk, J.P.

    1999-01-01

    PURPOSE: The purpose of this study was to gain insight into the importance of stimulation dynamics for force development in human vertical jumping. METHODS: Maximum height squat jumps were performed by 21 male subjects. As a measure of signal dynamics, rise time (RT) was used, i.e., the time taken

  18. Probing new light force-mediators by isotope shift spectroscopy

    International Nuclear Information System (INIS)

    Berengut, Julian C.; Budker, Dmitry; California Univ., Berkeley, CA; Lawrence Berkeley National Laboratory, Berkeley, CA; Delaunay, Cedric

    2017-04-01

    In this Letter we explore the potential of probing new light force-carriers, with spin-independent couplings to the electron and the neutron, using precision isotope shift spectroscopy. We develop a formalism to interpret linear King plots as bounds on new physics with minimal theory inputs. We focus only on bounding the new physics contributions that can be calculated independently of the Standard Model nuclear effects. We apply our method to existing Ca"+ data and project its sensitivity to possibly existing new bosons using narrow transitions in other atoms and ions (specifically, Sr and Yb). Future measurements are expected to improve the relative precision by five orders of magnitude, and can potentially lead to an unprecedented sensitivity for bosons within the 10 keV to 10 MeV mass range.

  19. Probing new light force-mediators by isotope shift spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Berengut, Julian C. [New South Wales Univ., Sydney, NSW (Australia). School of Physics; Budker, Dmitry [Mainz Univ. (Germany). Helmholtz-Inst. Mainz; California Univ., Berkeley, CA (United States). Physics Dept.; Lawrence Berkeley National Laboratory, Berkeley, CA (United States). Nuclear Science Div.; Delaunay, Cedric [Savoie Mont Blanc Univ., Annecy-le-Vieux (France). Laboratoire d' Annecy-le-Vieux de Physique Theorique LAPTh; and others

    2017-04-15

    In this Letter we explore the potential of probing new light force-carriers, with spin-independent couplings to the electron and the neutron, using precision isotope shift spectroscopy. We develop a formalism to interpret linear King plots as bounds on new physics with minimal theory inputs. We focus only on bounding the new physics contributions that can be calculated independently of the Standard Model nuclear effects. We apply our method to existing Ca{sup +} data and project its sensitivity to possibly existing new bosons using narrow transitions in other atoms and ions (specifically, Sr and Yb). Future measurements are expected to improve the relative precision by five orders of magnitude, and can potentially lead to an unprecedented sensitivity for bosons within the 10 keV to 10 MeV mass range.

  20. Exploring the energy landscape of biopolymers using single molecule force spectroscopy and molecular simulations

    OpenAIRE

    Hyeon, Changbong

    2010-01-01

    In recent years, single molecule force techniques have opened a new avenue to decipher the folding landscapes of biopolymers by allowing us to watch and manipulate the dynamics of individual proteins and nucleic acids. In single molecule force experiments, quantitative analyses of measurements employing sound theoretical models and molecular simulations play central role more than any other field. With a brief description of basic theories for force mechanics and molecular simulation techniqu...

  1. Characterisation of cellular adhesion reinforcement by multiple bond force spectroscopy in alveolar epithelial cells.

    Science.gov (United States)

    Nguyen, Ngoc-Minh; Angely, Christelle; Andre Dias, Sofia; Planus, Emmanuelle; Filoche, Marcel; Pelle, Gabriel; Louis, Bruno; Isabey, Daniel

    2017-07-01

    Integrin-mediated adhesion is a key process by which cells physically connect with their environment, and express sensitivity and adaptation through mechanotransduction. A critical step of cell adhesion is the formation of the first bonds which individually generate weak contacts (∼tens pN) but can sustain thousand times higher forces (∼tens nN) when associated. We propose an experimental validation by multiple bond force spectroscopy (MFS) of a stochastic model predicting adhesion reinforcement permitted by non-cooperative, multiple bonds on which force is homogeneously distributed (called parallel bond configuration). To do so, spherical probes (diameter: 6.6 μm), specifically coated by RGD-peptide to bind integrins, are used to statically indent and homogenously stretch the multiple bonds created for short contact times (2 s) between the bead and the surface of epithelial cells (A549). Using different separation speeds (v = 2, 5, 10 μm/s) and measuring cellular Young's modulus as well as the local stiffness preceding local rupture events, we obtain cell-by-cell the effective loading rates both at the global cell level and at the local level of individual constitutive bonds. Local rupture forces are in the range: f*=60-115 pN , whereas global rupture (detachment) forces reach F*=0.8-1.7 nN . Global and local rupture forces both exhibit linear dependencies with the effective loading rate, the slopes of these two linear relationships providing an estimate of the number of independent integrin bonds constituting the tested multiple bond structure (∼12). The MFS method enables to validate the reinforcement of integrin-mediated adhesion induced by the multiple bond configuration in which force is homogeneously distributed amongst parallel bonds. Local rupture events observed in the course of a spectroscopy manoeuver (MFS) lead to rupture force values considered in the literature as single-integrin bonds. Adhesion reinforcement permitted by the parallel

  2. Complex dynamics and switching transients in periodically forced Filippov prey–predator system

    International Nuclear Information System (INIS)

    Tang, Guangyao; Qin, Wenjie; Tang, Sanyi

    2014-01-01

    Highlights: •We develop a Filippov prey–predator model with periodic forcing. •The sliding mode dynamics and its domain have been investigated. •The existence and stability of sliding periodic solution have been discussed. •The complex dynamics are addressed through bifurcation analyses. •Switching transients and their biological implications have been discussed. - Abstract: By employing threshold policy control (TPC) in combination with the definition of integrated pest management (IPM), a Filippov prey–predator model with periodic forcing has been proposed and studied, and the periodic forcing is affected by assuming a periodic variation in the intrinsic growth rate of the prey. This study aims to address how the periodic forcing and TPC affect the pest control. To do this, the sliding mode dynamics and sliding mode domain have been addressed firstly by using Utkin’s equivalent control method, and then the existence and stability of sliding periodic solution are investigated. Furthermore, the complex dynamics including multiple attractors coexistence, period adding sequences and chaotic solutions with respect to bifurcation parameters of forcing amplitude and economic threshold (ET) have been investigated numerically in more detail. Finally the switching transients associated with pest outbreaks and their biological implications have been discussed. Our results indicate that the sliding periodic solution could be globally stable, and consequently the prey or pest population can be controlled such that its density falls below the economic injury level (EIL). Moreover, the switching transients have both advantages and disadvantages concerning pest control, and the magnitude and frequency of switching transients depend on the initial values of both populations, forcing amplitude and ET

  3. Exploring process dynamics by near infrared spectroscopy in lactic fermentations

    DEFF Research Database (Denmark)

    Svendsen, Carina; Cieplak, Tomasz; van der Berg, Franciscus Winfried J

    2016-01-01

    In the industrial production of yoghurt, measurement of pH is normally the only in-line technique applied as a real-time monitoring signalfor following the dynamics during the fermentation process. However, every dairy company would benefit from an in-line technique giving information about...... the chemical composition, physical/textural properties and/or microbial contamination. In this study lactic fermentation batches with the starter bacteria Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus are explored by in-line near infrared (NIR) spectroscopy. The dynamics obtained...

  4. 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.

  5. 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.

  6. Traction force dynamics predict gap formation in activated endothelium

    International Nuclear Information System (INIS)

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

    2016-01-01

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

  7. Traction force dynamics predict gap formation in activated endothelium

    Energy Technology Data Exchange (ETDEWEB)

    Valent, Erik T.; Nieuw Amerongen, Geerten P. van; Hinsbergh, Victor W.M. van; Hordijk, Peter L., E-mail: p.hordijk@vumc.nl

    2016-09-10

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

  8. Grip Force Adjustments Reflect Prediction of Dynamic Consequences in Varying Gravitoinertial Fields

    Directory of Open Access Journals (Sweden)

    Olivier White

    2018-02-01

    Full Text Available Humans have a remarkable ability to adjust the way they manipulate tools through a genuine regulation of grip force according to the task. However, rapid changes in the dynamical context may challenge this skill, as shown in many experimental approaches. Most experiments adopt perturbation paradigms that affect only one sensory modality. We hypothesize that very fast adaptation can occur if coherent information from multiple sensory modalities is provided to the central nervous system. Here, we test whether participants can switch between different and never experienced dynamical environments induced by centrifugation of the body. Seven participants lifted an object four times in a row successively in 1, 1.5, 2, 2.5, 2, 1.5, and 1 g. We continuously measured grip force, load force and the gravitoinertial acceleration that was aligned with body axis (perceived gravity. Participants adopted stereotyped grasping movements immediately upon entry in a new environment and needed only one trial to adapt grip forces to a stable performance in each new gravity environment. This result was underlined by good correlations between grip and load forces in the first trial. Participants predictively applied larger grip forces when they expected increasing gravity steps. They also decreased grip force when they expected decreasing gravity steps, but not as much as they could, indicating imperfect anticipation in that condition. The participants' performance could rather be explained by a combination of successful scaling of grip force according to gravity changes and a separate safety factor. The data suggest that in highly unfamiliar dynamic environments, grip force regulation is characterized by a combination of a successful anticipation of the experienced environmental condition, a safety factor reflecting strategic response to uncertainties about the environment and rapid feedback mechanisms to optimize performance under constant conditions.

  9. Subharmonic Oscillations and Chaos in Dynamic Atomic Force Microscopy

    Science.gov (United States)

    Cantrell, John H.; Cantrell, Sean A.

    2015-01-01

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

  10. Satellite Dynamic Damping via Active Force Control Augmentation

    Science.gov (United States)

    Varatharajoo, Renuganth

    2012-07-01

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

  11. State-Resolved Metal Nanoparticle Dynamics Viewed through the Combined Lenses of Ultrafast and Magneto-optical Spectroscopies.

    Science.gov (United States)

    Zhao, Tian; Herbert, Patrick J; Zheng, Hongjun; Knappenberger, Kenneth L

    2018-05-08

    Electronic carrier dynamics play pivotal roles in the functional properties of nanomaterials. For colloidal metals, the mechanisms and influences of these dynamics are structure dependent. The coherent carrier dynamics of collective plasmon modes for nanoparticles (approximately 2 nm and larger) determine optical amplification factors that are important to applied spectroscopy techniques. In the nanocluster domain (sub-2 nm), carrier coupling to vibrational modes affects photoluminescence yields. The performance of photocatalytic materials featuring both nanoparticles and nanoclusters also depends on the relaxation dynamics of nonequilibrium charge carriers. The challenges for developing comprehensive descriptions of carrier dynamics spanning both domains are multifold. Plasmon coherences are short-lived, persisting for only tens of femtoseconds. Nanoclusters exhibit discrete carrier dynamics that can persist for microseconds in some cases. On this time scale, many state-dependent processes, including vibrational relaxation, charge transfer, and spin conversion, affect carrier dynamics in ways that are nonscalable but, rather, structure specific. Hence, state-resolved spectroscopy methods are needed for understanding carrier dynamics in the nanocluster domain. Based on these considerations, a detailed understanding of structure-dependent carrier dynamics across length scales requires an appropriate combination of spectroscopic methods. Plasmon mode-specific dynamics can be obtained through ultrafast correlated light and electron microscopy (UCLEM), which pairs interferometric nonlinear optical (INLO) with electron imaging methods. INLO yields nanostructure spectral resonance responses, which capture the system's homogeneous line width and coherence dynamics. State-resolved nanocluster dynamics can be obtained by pairing ultrafast with magnetic-optical spectroscopy methods. In particular, variable-temperature variable-field (VTVH) spectroscopies allow quantification

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

    Science.gov (United States)

    Ver, Istvan L.; Howe, Michael S.

    1994-01-01

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

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

    Science.gov (United States)

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

    2009-01-01

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

  14. Forced fluid dynamics from blackfolds in general supergravity backgrounds

    Energy Technology Data Exchange (ETDEWEB)

    Armas, Jay [Physique Théorique et Mathématique,Université Libre de Bruxelles and International Solvay Institutes,ULB-Campus Plaine CP231, B-1050 Brussels (Belgium); Gath, Jakob [Centre de Physique Théorique, École Polytechnique,CNRS UMR 7644, Université Paris-Saclay,F-91128 Palaiseau (France); Niarchos, Vasilis [Crete Center for Theoretical Physics, Institute of Theoretical and Computational Physics,Crete Center for Quantum Complexity and Nanotechnology,Department of Physics, University of Crete,Heraklion, 71303 (Greece); Obers, Niels A.; Pedersen, Andreas Vigand [The Niels Bohr Institute, Copenhagen University,Blegdamsvej 17, DK-2100 Copenhagen Ø (Denmark)

    2016-10-27

    We present a general treatment of the leading order dynamics of the collective modes of charged dilatonic p-brane solutions of (super)gravity theories in arbitrary backgrounds. To this end we employ the general strategy of the blackfold approach which is based on a long-wavelength derivative expansion around an exact or approximate solution of the (super)gravity equations of motion. The resulting collective mode equations are formulated as forced hydrodynamic equations on dynamically embedded hypersurfaces. We derive them in full generality (including all possible asymptotic fluxes and dilaton profiles) in a far-zone analysis of the (super)gravity equations and in representative examples in a near-zone analysis. An independent treatment based on the study of external couplings in hydrostatic partition functions is also presented. Special emphasis is given to the forced collective mode equations that arise in type IIA/B and eleven-dimensional supergravities, where besides the standard Lorentz force couplings our analysis reveals additional couplings to the background, including terms that arise from Chern-Simons interactions. We also present a general overview of the blackfold approach and some of the key conceptual issues that arise when applied to arbitrary backgrounds.

  15. Role of attractive forces in determining the equilibrium structure and dynamics of simple liquids

    DEFF Research Database (Denmark)

    Toxværd, Søren

    2015-01-01

    Molecular Dynamics simulations of a Lennard-Jones system with different range of attraction show that the attractive forces modify the radial distribution of the particles. For condensed liquids only, the forces within the the first coordination shell (FCS) are important, but for gases and moderate...... condensed fluids, even the attractive forces outside the FCS play a role. The changes in the distribution caused by neglecting the attractive forces, lead to a too high pressure. The weak long-range attractions damp the dynamics and the diffusion of the particles in gas-, super critical fluid- and in liquid...

  16. 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.

  17. Modeling of Dynamic Fluid Forces in Fast Switching Valves

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  18. Cellular dynamics of bovine aortic smooth muscle cells measured using MEMS force sensors

    Science.gov (United States)

    Tsukagoshi, Takuya; Nguyen, Thanh-Vinh; Hirayama Shoji, Kayoko; Takahashi, Hidetoshi; Matsumoto, Kiyoshi; Shimoyama, Isao

    2018-04-01

    Adhesive cells perceive the mechanical properties of the substrates to which they adhere, adjusting their cellular mechanical forces according to their biological characteristics. This mechanical interaction subsequently affects the growth, locomotion, and differentiation of the cell. However, little is known about the detailed mechanism that underlies this interaction between adherent cells and substrates because dynamically measuring mechanical phenomena is difficult. Here, we utilize microelectromechamical systems force sensors that can measure cellular traction forces with high temporal resolution (~2.5 µs) over long periods (~3 h). We found that the cellular dynamics reflected physical phenomena with time scales from milliseconds to hours, which contradicts the idea that cellular motion is slow. A single focal adhesion (FA) generates an average force of 7 nN, which disappears in ms via the action of trypsin-ethylenediaminetetraacetic acid. The force-changing rate obtained from our measurements suggests that the time required for an FA to decompose was nearly proportional to the force acting on the FA.

  19. Dynamic fracture mechanics with electromagnetic force and its application to fracture toughness and testing

    International Nuclear Information System (INIS)

    Yagawa, G.; Yoshimura, S.

    1986-01-01

    This study is concerned with the application of the electromagnetic force to the determination of the dynamic fracture toughness of materials. Taken is an edge-cracked specimen which carries a transient electric current I and is simply supported in a uniform and steady magnetic field B. As a result of their interaction, the dynamic electromagnetic force occurs in the whole body of the specimen, which is then deformed to fracture in the opening mode of cracking. For the evaluation of dynamic fracture toughness, the extended J integral with the effects of the electromagnetic force and inertia is calculated using the dynamic finite-element method. To determine the dynamic crack-initiation point in the experiment, the electric potential method is used in the case of brittle fracture, and the electric potential and the J-R curve methods in the case of ductile fracture, respectively. Using these techniques, the dynamic fracture toughness values of nuclear pressure vessel steel A508 class 3 are evaluated over a wide temperature range. (author)

  20. ON THE DYNAMIC VERTICAL WHEEL-RAIL FORCES AT LOW FREQUENCIES

    Directory of Open Access Journals (Sweden)

    Mădălina DUMITRIU

    2012-05-01

    Full Text Available To homologate the railay vehicles, from the pespective of dynamic behavior, the dynamic forces generated at the wheel/rail interface should be limited, in order to comply with the criterion regarding the rolling track fatigue. The meeting of this requirement implies the vehicle adjustment in its construction. This paper examines the influence of certain vehicle parameters upon the magnitude of the dynamic vertical loads derived during travelling on a track with random irregularities. It will be shown how the minimizing condition of the dynamic vertical loads can result into the best primary suspension damping

  1. Irreversible energy flow in forced Vlasov dynamics

    KAUST Repository

    Plunk, Gabriel G.; Parker, Joseph T.

    2014-01-01

    © EDP Sciences, Società Italiana di Fisica, Springer-Verlag. The recent paper of Plunk [G.G. Plunk, Phys. Plasmas 20, 032304 (2013)] considered the forced linear Vlasov equation as a model for the quasi-steady state of a single stable plasma wavenumber interacting with a bath of turbulent fluctuations. This approach gives some insight into possible energy flows without solving for nonlinear dynamics. The central result of the present work is that the forced linear Vlasov equation exhibits asymptotically zero (irreversible) dissipation to all orders under a detuning of the forcing frequency and the characteristic frequency associated with particle streaming. We first prove this by direct calculation, tracking energy flow in terms of certain exact conservation laws of the linear (collisionless) Vlasov equation. Then we analyze the steady-state solutions in detail using a weakly collisional Hermite-moment formulation, and compare with numerical solution. This leads to a detailed description of the Hermite energy spectrum, and a proof of no dissipation at all orders, complementing the collisionless Vlasov result.

  2. Irreversible energy flow in forced Vlasov dynamics

    KAUST Repository

    Plunk, Gabriel G.

    2014-10-01

    © EDP Sciences, Società Italiana di Fisica, Springer-Verlag. The recent paper of Plunk [G.G. Plunk, Phys. Plasmas 20, 032304 (2013)] considered the forced linear Vlasov equation as a model for the quasi-steady state of a single stable plasma wavenumber interacting with a bath of turbulent fluctuations. This approach gives some insight into possible energy flows without solving for nonlinear dynamics. The central result of the present work is that the forced linear Vlasov equation exhibits asymptotically zero (irreversible) dissipation to all orders under a detuning of the forcing frequency and the characteristic frequency associated with particle streaming. We first prove this by direct calculation, tracking energy flow in terms of certain exact conservation laws of the linear (collisionless) Vlasov equation. Then we analyze the steady-state solutions in detail using a weakly collisional Hermite-moment formulation, and compare with numerical solution. This leads to a detailed description of the Hermite energy spectrum, and a proof of no dissipation at all orders, complementing the collisionless Vlasov result.

  3. Dual time-resolved temperature-jump fluorescence and infrared spectroscopy for the study of fast protein dynamics.

    Science.gov (United States)

    Davis, Caitlin M; Reddish, Michael J; Dyer, R Brian

    2017-05-05

    Time-resolved temperature-jump (T-jump) coupled with fluorescence and infrared (IR) spectroscopy is a powerful technique for monitoring protein dynamics. Although IR spectroscopy of the polypeptide amide I mode is more technically challenging, it offers complementary information because it directly probes changes in the protein backbone, whereas, fluorescence spectroscopy is sensitive to the environment of specific side chains. With the advent of widely tunable quantum cascade lasers (QCL) it is possible to efficiently probe multiple IR frequencies with high sensitivity and reproducibility. Here we describe a dual time-resolved T-jump fluorescence and IR spectrometer and its application to study protein folding dynamics. A Q-switched Ho:YAG laser provides the T-jump source for both time-resolved IR and fluorescence spectroscopy, which are probed by a QCL and Ti:Sapphire laser, respectively. The Ho:YAG laser simultaneously pumps the time-resolved IR and fluorescence spectrometers. The instrument has high sensitivity, with an IR absorbance detection limit of jump induced difference spectrum from 50ns to 0.5ms. This study demonstrates the power of the dual time-resolved T-jump fluorescence and IR spectroscopy to resolve complex folding mechanisms by complementary IR absorbance and fluorescence measurements of protein dynamics. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Force-dynamic cultural models in a scalar adjectival construction

    DEFF Research Database (Denmark)

    Jensen, Kim Ebensgaard

    MAG NationalGeographic) (3) If the making of a revolution is drama, punctuated with tragedies too numerous to count, making peace is long-form prose requiring iterations of conversation between people. (COCA 2011 MAG TechReview) (4) I'm too young to get married. (COCA 2011 FIC Callaloo) (5) I......'m in a certain group that's almost too old to hire. (COCA 2011 NEWS Denver) (6) Mr. Turman insisted he was too busy to meet at any other time. (COCA 2011 NEWS NYTimes) In all instances, semantic relations of force-dynamics are set up between the adjective and verb positions, such that the adjective describes...... that the constructional semantics may interact with underlying cultural models (Holland & Quinn 1987, Ungerer & Schmid 2006: 51-59) of force-dynamics or causation (d'Andrade 1987: 117-118). In their study of the English into-causative, Gries & Stefanowitsch (2004: 232-234) suggest that collexeme combinations...

  5. Force Spectroscopy of the Plasmodium falciparum Vaccine Candidate Circumsporozoite Protein Suggests a Mechanically Pliable Repeat Region.

    Science.gov (United States)

    Patra, Aditya Prasad; Sharma, Shobhona; Ainavarapu, Sri Rama Koti

    2017-02-10

    The most effective vaccine candidate of malaria is based on the Plasmodium falciparum circumsporozoite protein (CSP), a major surface protein implicated in the structural strength, motility, and immune evasion properties of the infective sporozoites. It is suspected that reversible conformational changes of CSP are required for infection of the mammalian host, but the detailed structure and dynamic properties of CSP remain incompletely understood, limiting our understanding of its function in the infection. Here, we report the structural and mechanical properties of the CSP studied using single-molecule force spectroscopy on several constructs, one including the central region of CSP, which is rich in NANP amino acid repeats (CSP rep ), and a second consisting of a near full-length sequence without the signal and anchor hydrophobic domains (CSP ΔHP ). Our results show that the CSP rep is heterogeneous, with 40% of molecules requiring virtually no mechanical force to unfold (<10 piconewtons (pN)), suggesting that these molecules are mechanically compliant and perhaps act as entropic springs, whereas the remaining 60% are partially structured with low mechanical resistance (∼70 pN). CSP ΔHP having multiple force peaks suggests specifically folded domains, with two major populations possibly indicating the open and collapsed forms. Our findings suggest that the overall low mechanical resistance of the repeat region, exposed on the outer surface of the sporozoites, combined with the flexible full-length conformations of CSP, may provide the sporozoites not only with immune evasion properties, but also with lubricating capacity required during its navigation through the mosquito and vertebrate host tissues. We anticipate that these findings would further assist in the design and development of future malarial vaccines. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Measuring protein dynamics with ultrafast two-dimensional infrared spectroscopy

    International Nuclear Information System (INIS)

    Adamczyk, Katrin; Candelaresi, Marco; Hunt, Neil T; Robb, Kirsty; Hoskisson, Paul A; Tucker, Nicholas P; Gumiero, Andrea; Walsh, Martin A; Parker, Anthony W

    2012-01-01

    Recent advances in the methodology and application of ultrafast two-dimensional infrared (2D-IR) spectroscopy to biomolecular systems are reviewed. A description of the 2D-IR technique and the molecular contributions to the observed spectra are presented followed by a discussion of recent literature relating to the use of 2D-IR and associated approaches for measuring protein dynamics. In particular, these include the use of diatomic ligand groups for measuring haem protein dynamics, isotopic labelling strategies and the use of vibrational probe groups. The final section reports on the current state of the art regarding the use of 2D-IR methods to provide insights into biological reaction mechanisms. (topical review)

  7. Investigation of Calibrating Force Transducer Using Sinusoidal Force

    International Nuclear Information System (INIS)

    Zhang Li; Wang Yu; Zhang Lizhe

    2010-01-01

    Sinusoidal force calibration method was studied several years before at Physikalisch-Technische Bundesanstalt (PTB). A similar dynamic force calibration system is developed at Changcheng Institute of Metrology and Measurement (CIMM). It uses electro-dynamic shakers to generate dynamic force in the range from 1 N to 20 kN, and heterodyne laser interferometers are used for acceleration measurement. The force transducer to be calibrated is mounted on the shaker, and a mass block is screwed on the top of force transducer, the sinusoidal forces realized by accelerated load masses are traceable to acceleration and mass according to the force definition. The methods of determining Spatial-dependent acceleration on mass block and measuring the end mass of force transducer in dynamic force calibration are discussed in this paper.

  8. Influence of forced respiration on nonlinear dynamics in heart rate variability

    DEFF Research Database (Denmark)

    Kanters, J K; Højgaard, M V; Agner, E

    1997-01-01

    Although it is doubtful whether the normal sinus rhythm can be described as low-dimensional chaos, there is evidence for inherent nonlinear dynamics and determinism in time series of consecutive R-R intervals. However, the physiological origin for these nonlinearities is unknown. The aim...... with a metronome set to 12 min(-1). Nonlinear dynamics were measured as the correlation dimension and the nonlinear prediction error. Complexity expressed as correlation dimension was unchanged from normal respiration, 9.1 +/- 0.5, compared with forced respiration, 9.3 +/- 0.6. Also, nonlinear determinism...... expressed as the nonlinear prediction error did not differ between spontaneous respiration, 32.3 +/- 3.4 ms, and forced respiration, 31.9 +/- 5.7. It is concluded that the origin of the nonlinear dynamics in heart rate variability is not a nonlinear input from the respiration into the cardiovascular...

  9. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

    DEFF Research Database (Denmark)

    Maragakis, Paul; Lindorff-Larsen, Kresten; Eastwood, Michael P

    2008-01-01

    . Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration......A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure...... methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared...

  10. Tip-surface interactions at redox responsive poly(ferrocenylsilane) (PFS) interface by AFM-based force spectroscopy

    International Nuclear Information System (INIS)

    Chung Hongjing; Song Jing; Vancso, G. Julius

    2009-01-01

    Poly(ferrocenylsilanes) (PFS) belong to the class of redox responsive organometallic polymers. Atomic force microscopy (AFM)-based single molecule force spectroscopy (SMFS) was used earlier to study single chain PFS response and redox energy driven single chain PFS molecular motors. Here we present further AFM investigations of force interactions between tip and a grafted PFS surface under potential control in electrochemical redox cycles. Typical tip-Au interaction is considered as reference in the force measurements. First the electrostatic component in the diffused double layer (DL) in NaClO 4 electrolyte environment was considered for a 'grafted to' PFS, which dominated the interplay between the tip and sample surface. The DL forces can also hinder the physisorption of PFS chain onto the tip when the voltage was applied at -0.1 V. On the other hand, if the tip contacted the PFS surface prior to the electrochemical process, physisorption of PFS chains governed the overall interaction regardless of subsequently applied surface potential. In addition, prolonged contact time, t c , may also contribute to the stability of tip-PFS bridging and detection of electrostatic forces between the tip-PFS interface. The results showed that tip-substrate interaction forces without PFS grafts have negligibly small force contributions under similar, electrochemically controlled, conditions used in single PFS chain based molecular motors.

  11. On-site Identification of Dynamic Annular Seal Forces in Turbo Machinery Using Active Magnetic Bearings - An Experimental Investigation

    DEFF Research Database (Denmark)

    Lauridsen, Jonas S.; Santos, Ilmar F.

    2017-01-01

    Significant dynamic forces can be generated by annular seals in rotordynamics and can under certain conditions destabilize the system leading to machine failure. Mathematical modelling of dynamic seal forces are still challenging, especially for multiphase fluids and for seals with complex...... geometries. This results in much uncertainty in the estimation of the dynamic seal forces which often leads to unexpected system behaviour. This paper presents the results of a method suitable for on-site identification of uncertain dynamic annular seal forces in rotordynamic systems supported by Active...... Magnetic Bearings (AMB). An excitation current is applied through the AMBs to obtain perturbation forces and a system response, from which, the seal coefficients are extracted by utilizing optimization and a-priori information about the mathematical model structure and its known system dynamics. As a study...

  12. Dynamics of the Bogie of Maglev Train with Distributed Magnetic Forces

    Directory of Open Access Journals (Sweden)

    Yaozong Liu

    2015-01-01

    Full Text Available A dynamic model of the bogie of maglev train with distributed magnetic forces and four identical levitating controllers is formulated. The vertical, pitching, and rolling degree of freedom of the electromagnet modules and their coupling are considered. The frequency responses of the bogie to track irregularity are investigated with numerical simulation. The results tell us that there are resonances related to the first electromagnetic suspension whose frequencies are determined by the control parameters. A comparative analysis has been carried out between the models with distributed or concentrated magnetic forces. The comparison indicates that simplifying the distributed magnetic force to concentrated one degenerates the dynamic behavior of the maglev bogie, especially resulting in overestimated resonances of the first electromagnetic suspension of maglev trains. The results also indicate that those resonances only occur on specific wavelengths of irregularity that relate to the length of the electromagnets.

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

    Science.gov (United States)

    Knoop, Claas; Fritsching, Udo

    2014-03-01

    In this paper the acoustic forces on particles and agglomerates caused by high-intensity ultrasound in gaseous atmosphere are derived by means of computational fluid dynamics (CFD). Sound induced forces cause an oscillating stress scenario where the primary particles of an agglomerate are alternatingly pressed together and torn apart with the frequency of the applied wave. A comparison of the calculated acoustic forces with respect to the inter particle adhesion forces from Van-der-Waals and liquid bridge interactions reveals that the separation forces may reach the same order of magnitude for 80 μm sized SiO2-particles. Hence, with finite probability acoustically agitated gases may de-agglomerate/disperse solid agglomerate structures. This effect is confirmed by dispersion experiments in an acoustic particle levitation setup. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. CONTIN XPCS: Software for Inverse Transform Analysis of X-Ray Photon Correlation Spectroscopy Dynamics.

    Science.gov (United States)

    Andrews, Ross N; Narayanan, Suresh; Zhang, Fan; Kuzmenko, Ivan; Ilavsky, Jan

    2018-02-01

    X-ray photon correlation spectroscopy (XPCS) and dynamic light scattering (DLS) both reveal dynamics using coherent scattering, but X-rays permit investigating of dynamics in a much more diverse array of materials. Heterogeneous dynamics occur in many such materials, and we showed how classic tools employed in analysis of heterogeneous DLS dynamics extend to XPCS, revealing additional information that conventional Kohlrausch exponential fitting obscures. This work presents the software implementation of inverse transform analysis of XPCS data called CONTIN XPCS, an extension of traditional CONTIN that accommodates dynamics encountered in equilibrium XPCS measurements.

  15. A Piezoelectric PZT Ceramic Mulitlayer Stack for Energy Harvesting Under Dynamic Forces

    Science.gov (United States)

    Xu, Tian-Bing; Siochi, Emilie J.; Kang, Jin Ho; Zuo, Lei; Zhou, Wanlu; Tang, Xiudong; Jiang, Xiaoning

    2011-01-01

    Piezoelectric energy harvesting transducers (PEHTs) are commonly used in motion/vibration energy scavenging devices. To date, most researchers have focused on energy harvesting at narrow bandwidths around the mechanical resonance frequency, and most piezoelectric harvesting devices reported in the literature have very low effective piezoelectric coefficient (d(sub eff)) (PZT ceramic multilayer stack (PZT-Stack) with high effective piezoelectric coefficient for high-performance PEHTs. The PZT-Stack is composed of 300 layers of 0.1 mm thick PZT plates, with overall dimensions of 32.4 mm X 7.0 mm X 7.0 mm. Experiments were carried out with dynamic forces in a broad bandwidth ranging from 0.5 Hz to 25 kHz. The measured results show that the effective piezoelectric coefficient of the PZT-stack is about 1 X 10(exp 5) pC/N at off-resonance frequencies and 1.39 X 10(exp 6) pC/N at resonance, which is order of magnitude larger than that of traditional PEHTs. The effective piezoelectric coefficients (d(sub eff)) do not change significantly with applied dynamic forces having root mean square (RMS) values ranging from 1 N to 40 N. In resonance mode, 231 mW of electrical power was harvested at 2479 Hz with a dynamic force of 11.6 N(sub rms), and 7.6 mW of electrical power was generated at a frequency of 2114 Hz with 1 N(sub rms) dynamic force. In off-resonance mode, an electrical power of 18.7 mW was obtained at 680 Hz with a 40 N(sub rms) dynamic force. A theoretical model of energy harvesting for the PZT-Stack is established. The modeled results matched well with experimental measurements. This study demonstrated that high effective piezoelectric coefficient structures enable PEHTs to harvest more electrical energy from mechanical vibrations or motions, suggesting an effective design for high-performance low-footprint PEHTs with potential applications in military, aerospace, and portable electronics. In addition, this study provides a route for using piezoelectric multilayer

  16. Force adaptation transfers to untrained workspace regions in children: evidence for developing inverse dynamic motor models.

    Science.gov (United States)

    Jansen-Osmann, Petra; Richter, Stefanie; Konczak, Jürgen; Kalveram, Karl-Theodor

    2002-03-01

    When humans perform goal-directed arm movements under the influence of an external damping force, they learn to adapt to these external dynamics. After removal of the external force field, they reveal kinematic aftereffects that are indicative of a neural controller that still compensates the no longer existing force. Such behavior suggests that the adult human nervous system uses a neural representation of inverse arm dynamics to control upper-extremity motion. Central to the notion of an inverse dynamic model (IDM) is that learning generalizes. Consequently, aftereffects should be observable even in untrained workspace regions. Adults have shown such behavior, but the ontogenetic development of this process remains unclear. This study examines the adaptive behavior of children and investigates whether learning a force field in one hemifield of the right arm workspace has an effect on force adaptation in the other hemifield. Thirty children (aged 6-10 years) and ten adults performed 30 degrees elbow flexion movements under two conditions of external damping (negative and null). We found that learning to compensate an external damping force transferred to the opposite hemifield, which indicates that a model of the limb dynamics rather than an association of visited space and experienced force was acquired. Aftereffects were more pronounced in the younger children and readaptation to a null-force condition was prolonged. This finding is consistent with the view that IDMs in children are imprecise neural representations of the actual arm dynamics. It indicates that the acquisition of IDMs is a developmental achievement and that the human motor system is inherently flexible enough to adapt to any novel force within the limits of the organism's biomechanics.

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

    Science.gov (United States)

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

    2016-03-01

    Human dynamic models have been used to estimate joint kinetics during various activities. Kinetics estimation is in demand in sports and clinical applications where data on external forces, such as the ground reaction force (GRF), are not available. The purpose of this study was to estimate the GRF during gait by utilizing distance- and velocity-dependent force models between the foot and ground in an inverse-dynamics-based optimization. Ten males were tested as they walked at four different speeds on a force plate-embedded treadmill system. The full-GRF model whose foot-ground reaction elements were dynamically adjusted according to vertical displacement and anterior-posterior speed between the foot and ground was implemented in a full-body skeletal model. The model estimated the vertical and shear forces of the GRF from body kinematics. The shear-GRF model with dynamically adjustable shear reaction elements according to the input vertical force was also implemented in the foot of a full-body skeletal model. Shear forces of the GRF were estimated from body kinematics, vertical GRF, and center of pressure. The estimated full GRF had the lowest root mean square (RMS) errors at the slow walking speed (1.0m/s) with 4.2, 1.3, and 5.7% BW for anterior-posterior, medial-lateral, and vertical forces, respectively. The estimated shear forces were not significantly different between the full-GRF and shear-GRF models, but the RMS errors of the estimated knee joint kinetics were significantly lower for the shear-GRF model. Providing COP and vertical GRF with sensors, such as an insole-type pressure mat, can help estimate shear forces of the GRF and increase accuracy for estimation of joint kinetics. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Emergence of nonwhite noise in Langevin dynamics with magnetic Lorentz force

    Science.gov (United States)

    Chun, Hyun-Myung; Durang, Xavier; Noh, Jae Dong

    2018-03-01

    We investigate the low mass limit of Langevin dynamics for a charged Brownian particle driven by a magnetic Lorentz force. In the low mass limit, velocity variables relaxing quickly are coarse-grained out to yield effective dynamics for position variables. Without the Lorentz force, the low mass limit is equivalent to the high friction limit. Both cases share the same Langevin equation that is obtained by setting the mass to zero. The equivalence breaks down in the presence of the Lorentz force. The low mass limit cannot be achieved by setting the mass to zero. The limit is also distinct from the large friction limit. We derive the effective equations of motion in the low mass limit. The resulting stochastic differential equation involves a nonwhite noise whose correlation matrix has antisymmetric components. We demonstrate the importance of the nonwhite noise by investigating the heat dissipation by a driven Brownian particle, where the emergent nonwhite noise has a physically measurable effect.

  19. Static end-expiratory and dynamic forced expiratory tracheal collapse in COPD

    International Nuclear Information System (INIS)

    O'Donnell, C.R.; Bankier, A.A.; O'Donnell, D.H.; Loring, S.H.; Boiselle, P.M.

    2014-01-01

    Aim: To determine the range of tracheal collapse at end-expiration among chronic obstructive pulmonary disease (COPD) patients and to compare the extent of tracheal collapse between static end-expiratory and dynamic forced-expiratory multidetector-row computed tomography (MDCT). Materials and methods: After institutional review board approval and obtaining informed consent, 67 patients meeting the National Heart, Lung, and Blood Institute (NHLBI)/World Health Organization (WHO) Global Initiative for Chronic Obstructive Lung Disease (GOLD) criteria for COPD were sequentially imaged using a 64-detector-row CT machine at end-inspiration, during forced expiration, and at end-expiration. Standardized respiratory coaching and spirometric monitoring were employed. Mean percentage tracheal collapse at end-expiration and forced expiration were compared using correlation analysis, and the power of end-expiratory cross-sectional area to predict excessive forced-expiratory tracheal collapse was computed following construction of receiver operating characteristic (ROC) curves. Results: Mean percentage expiratory collapse among COPD patients was 17 ± 18% at end-expiration compared to 62 ± 16% during forced expiration. Over the observed range of end-expiratory tracheal collapse (approximately 10–50%), the positive predictive value of end-expiratory collapse to predict excessive (≥80%) forced expiratory tracheal collapse was <0.3. Conclusion: COPD patients demonstrate a wide range of end-expiratory tracheal collapse. The magnitude of static end-expiratory tracheal collapse does not predict excessive dynamic expiratory tracheal collapse

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

    International Nuclear Information System (INIS)

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

    2010-01-01

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

  1. Application of Solution NMR Spectroscopy to Study Protein Dynamics

    Directory of Open Access Journals (Sweden)

    Christoph Göbl

    2012-03-01

    Full Text Available Recent advances in spectroscopic methods allow the identification of minute fluctuations in a protein structure. These dynamic properties have been identified as keys to some biological processes. The consequences of this structural flexibility can be far‑reaching and they add a new dimension to the structure-function relationship of biomolecules. Nuclear Magnetic Resonance (NMR spectroscopy allows the study of structure as well as dynamics of biomolecules in a very broad range of timescales at atomic level. A number of new NMR methods have been developed recently to allow the measurements of time scales and spatial fluctuations, which in turn provide the thermodynamics associated with the biological processes. Since NMR parameters reflect ensemble measurements, structural ensemble approaches in analyzing NMR data have also been developed. These new methods in some instances can even highlight previously hidden conformational features of the biomolecules. In this review we describe several solution NMR methods to study protein dynamics and discuss their impact on important biological processes.

  2. Spectroscopy of Molecules in Extreme Rotational States Using AN Optical Centrifuge

    Science.gov (United States)

    Mullin, Amy S.; Toro, Carlos; Echibiri, Geraldine; Liu, Qingnan

    2012-06-01

    Our lab has developed a high-power optical centrifuge that is capable of trapping and spinning large number densities of molecules into extreme rotational states. By coupling this device with high resolution transient IR absorption spectroscopy, we measure the time-resolved behavior and energy profiles of individual ro-vibrational states of molecules in very high rotational states. Recent results will be discussed on the spectroscopy of new rotational states, collisional dynamics in the optical centrifuge, spatially-dependent energy profiles and possibilities for new chemistry induced by centrifugal forces.

  3. Relationship between maximum dynamic force of inferior members and body balance in strength training apprentices

    Directory of Open Access Journals (Sweden)

    Ariane Martins

    2010-08-01

    Full Text Available The relationship between force and balance show controversy results and has directimplications in exercise prescription practice. The objective was to investigate the relationshipbetween maximum dynamic force (MDF of inferior limbs and the static and dynamic balances.Participated in the study 60 individuals, with 18 to 24 years old, strength training apprentices.The MDF was available by mean the One Maximum Repetition (1MR in “leg press” and “kneeextension” and motor testes to available of static and dynamic balances. The correlation testsand multiple linear regression were applied. The force and balance variables showed correlationin females (p=0.038. The corporal mass and static balance showed correlation for the males(p=0.045. The explication capacity at MDF and practices time were small: 13% for staticbalance in males, 18% and 17%, respectively, for static and dynamic balance in females. Inconclusion: the MDF of inferior limbs showed low predictive capacity for performance in staticand dynamic balances, especially for males.

  4. Atomic force microscopy and spectroscopy to probe single membrane proteins in lipid bilayers.

    Science.gov (United States)

    Sapra, K Tanuj

    2013-01-01

    The atomic force microscope (AFM) has opened vast avenues hitherto inaccessible to the biological scientist. The high temporal (millisecond) and spatial (nanometer) resolutions of the AFM are suited for studying many biological processes in their native conditions. The AFM cantilever stylus is aptly termed as a "lab on a tip" owing to its versatility as an imaging tool as well as a handle to manipulate single bonds and proteins. Recent examples assert that the AFM can be used to study the mechanical properties and monitor processes of single proteins and single cells, thus affording insight into important mechanistic details. This chapter specifically focuses on practical and analytical protocols of single-molecule AFM methodologies related to high-resolution imaging and single-molecule force spectroscopy of membrane proteins. Both these techniques are operator oriented, and require specialized working knowledge of the instrument, theoretical, and practical skills.

  5. Microscopic Theory for the Role of Attractive Forces in the Dynamics of Supercooled Liquids.

    Science.gov (United States)

    Dell, Zachary E; Schweizer, Kenneth S

    2015-11-13

    We formulate a microscopic, no adjustable parameter, theory of activated relaxation in supercooled liquids directly in terms of the repulsive and attractive forces within the framework of pair correlations. Under isochoric conditions, attractive forces can nonperturbatively modify slow dynamics, but at high enough density their influence vanishes. Under isobaric conditions, attractive forces play a minor role. High temperature apparent Arrhenius behavior and density-temperature scaling are predicted. Our results are consistent with recent isochoric simulations and isobaric experiments on a deeply supercooled molecular liquid. The approach can be generalized to treat colloidal gelation and glass melting, and other soft matter slow dynamics problems.

  6. Dynamic Forces between the Rails and the Wheels of Railway Vehicle

    Directory of Open Access Journals (Sweden)

    Zdravko Peran

    2016-02-01

    Full Text Available The process of acquisition of the measured dynamic values of forces between the rails and the wheels on the real measurement train and the train tracks. The conversion of the measured values into the matrices and vectors enables numerous exact qualitative and quantitative studies of the dynamic phenomena behaviour. The paper shows the possibilities of using MATLAB computer tool. All the commands in the software are given and explained. Calculating of the empirical, normal and cumulative distribution on an example of the lateral force is given in detail. The new software is exactly verified mathematically and qualified for any further use. The developed software is the tool for the development of other two phases: software for the exact automatic evaluation of the maximum values of the dynamic values and software for the automatic approval of vehicles and railway due to the driving safety, loading tracks and driving comfort compared to the limited values regarding UI C CODE 518.

  7. Spectroscopy, Kinetics, and Dynamics of Combustion Radicals

    Energy Technology Data Exchange (ETDEWEB)

    Nesbitt, David J. [Research/Professor

    2013-08-06

    Spectroscopy, kinetics and dynamics of jet cooled hydrocarbon transients relevant to the DOE combustion mission have been explored, exploiting i) high resolution IR lasers, ii) slit discharge sources for formation of jet cooled radicals, and iii) high sensitivity detection with direct laser absorption methods and near the quantum shot noise limit. What makes this combination powerful is that such transients can be made under high concentrations and pressures characteristic of actual combustion conditions, and yet with the resulting species rapidly cooled (T ≈10-15K) in the slit supersonic expansion. Combined with the power of IR laser absorption methods, this provides novel access to spectral detection and study of many critical combustion species.

  8. UMER: An analog computer for dynamics of swarms interacting via long-range forces

    International Nuclear Information System (INIS)

    Kishek, R.A.; Bai, G.; Bernal, S.; Feldman, D.; Godlove, T.F.; Haber, I.; O'Shea, P.G.; Quinn, B.; Papadopoulos, C.; Reiser, M.; Stratakis, D.; Tian, K.; Tobin, C.J.; Walter, M.

    2006-01-01

    Some of the most challenging and interesting problems in nature involve large numbers of objects or particles mutually interacting through long-range forces. Examples range from galaxies and plasmas to flocks of birds and traffic flow on a highway. Even in cases where the form of the interacting force is precisely known, such as the 1/r 2 -dependent Coulomb and gravitational forces, such problems present a formidable theoretical and modeling challenge for large numbers of interacting bodies. This paper reports on a newly constructed, scaled particle accelerator that will serve as an experimental testbed for the dynamics of swarms interacting through long-range forces. Primarily designed for intense beam dynamics studies for advanced accelerators, the University of Maryland Electron Ring (UMER) design is described in detail and an update on commissioning is provided. An example application to a system other than a charged particle beam is discussed

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  10. Interactions of Histone Acetyltransferase p300 with the Nuclear Proteins Histone and HMGB1, As Revealed by Single Molecule Atomic Force Spectroscopy.

    Science.gov (United States)

    Banerjee, S; Rakshit, T; Sett, S; Mukhopadhyay, R

    2015-10-22

    One of the important properties of the transcriptional coactivator p300 is histone acetyltransferase (HAT) activity that enables p300 to influence chromatin action via histone modulation. p300 can exert its HAT action upon the other nuclear proteins too--one notable example being the transcription-factor-like protein HMGB1, which functions also as a cytokine, and whose accumulation in the cytoplasm, as a response to tissue damage, is triggered by its acetylation. Hitherto, no information on the structure and stability of the complexes between full-length p300 (p300FL) (300 kDa) and the histone/HMGB1 proteins are available, probably due to the presence of unstructured regions within p300FL that makes it difficult to be crystallized. Herein, we have adopted the high-resolution atomic force microscopy (AFM) approach, which allows molecularly resolved three-dimensional contour mapping of a protein molecule of any size and structure. From the off-rate and activation barrier values, obtained using single molecule dynamic force spectroscopy, the biochemical proposition of preferential binding of p300FL to histone H3, compared to the octameric histone, can be validated. Importantly, from the energy landscape of the dissociation events, a model for the p300-histone and the p300-HMGB1 dynamic complexes that HAT forms, can be proposed. The lower unbinding forces of the complexes observed in acetylating conditions, compared to those observed in non-acetylating conditions, indicate that upon acetylation, p300 tends to weakly associate, probably as an outcome of charge alterations on the histone/HMGB1 surface and/or acetylation-induced conformational changes. To our knowledge, for the first time, a single molecule level treatment of the interactions of HAT, where the full-length protein is considered, is being reported.

  11. Component dynamics in polymer blends a combined QENS and dielectric spectroscopy investigation

    CERN Document Server

    Hofmann, S; Arbe, A; Colmenero, J; Faragó, B

    2002-01-01

    The individual dynamics of the two constituents of a binary polymer blend was studied by means of quasielastic neutron scattering and dielectric spectroscopy (DS). The combination of neutron spin-echo and backscattering techniques allowed us to cover the complete crossover from entropy-driven chain dynamics on mesoscopic scales to the alpha relaxation on local length scales. The observed blending effects on the respective relaxation times suggest a purely dynamic origin of the dynamic heterogeneity in polymer blends at temperatures well above the glass-transition temperature without the need to assume local phase separation. In contrast, the results from DS experiments towards much lower temperatures indicate systematic deviations of the segmental dynamics in the blend from its mean-field-like behavior at high temperatures. This additionally increases the dynamic heterogeneity in the segmental dynamics of the two components in the mixture. In the case of the chain dynamics, no similar effect could be observed...

  12. Standard practice for verification of constant amplitude dynamic forces in an axial fatigue testing system

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2008-01-01

    1.1 This practice covers procedures for the dynamic verification of cyclic force amplitude control or measurement accuracy during constant amplitude testing in an axial fatigue testing system. It is based on the premise that force verification can be done with the use of a strain gaged elastic element. Use of this practice gives assurance that the accuracies of forces applied by the machine or dynamic force readings from the test machine, at the time of the test, after any user applied correction factors, fall within the limits recommended in Section 9. It does not address static accuracy which must first be addressed using Practices E 4 or equivalent. 1.2 Verification is specific to a particular test machine configuration and specimen. This standard is recommended to be used for each configuration of testing machine and specimen. Where dynamic correction factors are to be applied to test machine force readings in order to meet the accuracy recommended in Section 9, the verification is also specific to the c...

  13. Single Cell Force Spectroscopy for Quantification of Cellular Adhesion on Surfaces

    Science.gov (United States)

    Christenson, Wayne B.

    Cell adhesion is an important aspect of many biological processes. The atomic force microscope (AFM) has made it possible to quantify the forces involved in cellular adhesion using a technique called single cell force spectroscopy (SCFS). AFM based SCFS offers versatile control over experimental conditions for probing directly the interaction between specific cell types and specific proteins, surfaces, or other cells. Transmembrane integrins are the primary proteins involved in cellular adhesion to the extra cellular matix (ECM). One of the chief integrins involved in the adhesion of leukocyte cells is alpha Mbeta2 (Mac-1). The experiments in this dissertation quantify the adhesion of Mac-1 expressing human embryonic kidney (HEK Mac-1), platelets, and neutrophils cells on substrates with different concentrations of fibrinogen and on fibrin gels and multi-layered fibrinogen coated fibrin gels. It was shown that multi-layered fibrinogen reduces the adhesion force of these cells considerably. A novel method was developed as part of this research combining total internal reflection microscopy (TIRFM) with SCFS allowing for optical microscopy of HEK Mac-1 cells interacting with bovine serum albumin (BSA) coated glass after interacting with multi-layered fibrinogen. HEK Mac-1 cells are able to remove fibrinogen molecules from the multi-layered fibrinogen matrix. An analysis methodology for quantifying the kinetic parameters of integrin-ligand interactions from SCFS experiments is proposed, and the kinetic parameters of the Mac-1 fibrinogen bond are quantified. Additional SCFS experiments quantify the adhesion of macrophages and HEK Mac-1 cells on functionalized glass surfaces and normal glass surfaces. Both cell types show highest adhesion on a novel functionalized glass surface that was prepared to induce macrophage fusion. These experiments demonstrate the versatility of AFM based SCFS, and how it can be applied to address many questions in cellular biology offering

  14. Ionomer Dynamics: Insights from Broadband Dielectric Spectroscopy

    Science.gov (United States)

    Runt, James

    2015-03-01

    Ionomers (polymers containing ionic functionality) have been traditionally used as packaging materials and in molding applications, and are now of increasing interest as candidate single ion conductors for energy storage devices, in energy conversion, and for other electroactive materials applications. The focus of this presentation is on the insight that broadband dielectric (impedance) spectroscopy brings to our understanding of ion and polymer dynamics of this family of materials. As an example of our recent work on relatively conductive ionomers, the first portion of the presentation will focus on anion conducting polyphosphazene ionomers, in which polymer bound cations are quaternized with either short alkyl or short ether oxygen chains. The low Tg, amorphous nature, and cation-solvating backbone distinguish polyphosphazenes as promising materials for ion conduction, the iodide variants being of particular interest in solar cells. In the second part of this overview, the first findings on the molecular dynamics of linear precise polyethylene-based ionomers containing 1-methylimidazolium bromide pendants on exactly every 9th, 15th, or 21st carbon atom will be summarized. In order to develop a robust interpretation of the dynamics of these materials, it is imperative to develop a thorough understanding of microphase separation (e.g. ion aggregation), and each of the above studies is complimented by multiangle X-ray scattering experiments. Supported by the NSF Polymers Program and DOE Basic Energy Sciences.

  15. Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions

    International Nuclear Information System (INIS)

    Bradforth, S.E.

    1992-11-01

    The transition state region of a neutral bimolecular reaction may be experimentally investigated by photoelectron spectroscopy of an appropriate negative ion. The photoelectron spectrum provides information on the spectroscopy and dynamics of the short lived transition state and may be used to develop model potential energy surfaces that are semi-quantitative in this important region. The principles of bound → bound negative ion photoelectron spectroscopy are illustrated by way of an example: a full analysis of the photoelectron bands of CN - , NCO - and NCS - . Transition state photoelectron spectra are presented for the following systems Br + HI, Cl + HI, F + HI, F + CH 3 0H,F + C 2 H 5 OH,F + OH and F + H 2 . A time dependent framework for the simulation and interpretation of the bound → free transition state photoelectron spectra is subsequently developed and applied to the hydrogen transfer reactions Br + HI, F + OH → O( 3 P, 1 D) + HF and F + H 2 . The theoretical approach for the simulations is a fully quantum-mechanical wave packet propagation on a collinear model reaction potential surface. The connection between the wavepacket time evolution and the photoelectron spectrum is given by the time autocorrelation function. For the benchmark F + H 2 system, comparisons with three-dimensional quantum calculations are made

  16. Dynamics and Optimal Feet Force Distributions of a Realistic Four-legged Robot

    Directory of Open Access Journals (Sweden)

    Saurav Agarwal

    2012-08-01

    Full Text Available This paper presents a detailed dynamic modeling of realistic four-legged robot. The direct and inverse kinematic analysis for each leg has been considered in order to develop an overall kinematic model of the robot, when it follows a straight path. This study also aims to estimate optimal feet force distributions of the said robot, which is necessary for its real-time control. Three different approaches namely, minimization of norm of feet forces (approach 1, minimization of norm of joint torques (approach 2 and minimization of norm of joint power (approach 3 have been developed. Simulation result shows that approach 3 is more energy efficient foot force formulation than other two approaches. Lagrange-Euler formulation has been utilized to determine the joint torques. The developed dynamic models have been examined through computer simulation of continuous gait of the four-legged robot.

  17. Dynamics of normal and superfluid fogs using diffusing-wave spectroscopy

    International Nuclear Information System (INIS)

    Kim, Heetae; Lemieux, Pierre-Anthony; Durian, Douglas J.; Williams, Gary A.

    2004-01-01

    The dynamics of normal and superfluid fogs are studied using the technique of diffusing-wave spectroscopy. For a water fog generated with a 1.75 MHz piezoelectric driver below the liquid surface, the 7 μm diameter droplets are found to have diffusive dynamics for correlation times long compared to the viscous time. For a fog of 10 μm diameter superfluid helium droplets in helium vapor at 1.5 K the motion appears to be ballistic for correlation times short compared to the viscous time. The velocity correlations between the helium droplets are found to depend on the initial velocity with which the droplets are injected from the helium surface into the fog

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

    International Nuclear Information System (INIS)

    Xu, Rong-Guang; Leng, Yongsheng

    2016-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Rong-Guang; Leng, Yongsheng, E-mail: leng@gwu.edu [Department of Mechanical and Aerospace Engineering, The George Washington University, Washington, DC 20052 (United States)

    2016-04-21

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

  20. Importance of the CMAP Correction to the CHARMM22 Protein Force Field: Dynamics of Hen Lysozyme

    OpenAIRE

    Buck, Matthias; Bouguet-Bonnet, Sabine; Pastor, Richard W.; MacKerell, Alexander D.

    2005-01-01

    The recently developed CMAP correction to the CHARMM22 force field (C22) is evaluated from 25 ns molecular dynamics simulations on hen lysozyme. Substantial deviations from experimental backbone root mean-square fluctuations and N-H NMR order parameters obtained in the C22 trajectories (especially in the loops) are eliminated by the CMAP correction. Thus, the C22/CMAP force field yields improved dynamical and structural properties of proteins in molecular dynamics simulations.

  1. Direction-dependent force-induced dissociation dynamics of an entropic-driven lock-and-key assembly.

    Science.gov (United States)

    Chen, Yen-Fu; Chen, Hsuan-Yi; Sheng, Yu-Jane; Tsao, Heng-Kwong

    2017-09-01

    The unbinding dynamics of a nanosized sphere-and-cavity assembly under the pulling of constant force and constant loading rate is explored by dissipative particle dynamics simulations. The formation of this matched lock-and-key pair in a polymer solution is driven by the depletion attraction. The two-dimensional free energy landscape U(x,z) associated with this assembly is constructed. Our results indicate that the unbinding pathway along the orientation of the assembly is unfavorable due to the relatively high energy barrier compared to that along the tortuous minimum path whose energy barrier is not high. It is also found that the dissociation rate depends on the direction of the external force (θ) with respect to the assembly orientation. The presence of the force component perpendicular to the assembly orientation can reduce the bond lifetime significantly by driving the key particle to approach the minimum path. Moreover, the dissociation dynamics can be facilitated even by a pushing force compared to the spontaneous dissociation (without forces). To elucidate the effective pathway under pulling, the escaping position is analyzed and its mean direction with respect to the assembly orientation rises generally with increasing θ, revealing that the presence of the force component along the minimum pathway is helpful. The importance of the direction of the external pulling has been demonstrated in our simple system. Therefore, this effect should be considered in more complicated unbinding experiments.

  2. Dynamical-Decoupling-Based Quantum Sensing: Floquet Spectroscopy

    Directory of Open Access Journals (Sweden)

    J. E. Lang

    2015-10-01

    Full Text Available Sensing the internal dynamics of individual nuclear spins or clusters of nuclear spins has recently become possible by observing the coherence decay of a nearby electronic spin: the weak magnetic noise is amplified by a periodic, multipulse decoupling sequence. However, it remains challenging to robustly infer underlying atomic-scale structure from decoherence traces in all but the simplest cases. We introduce Floquet spectroscopy as a versatile paradigm for analysis of these experiments and argue that it offers a number of general advantages. In particular, this technique generalizes to more complex situations, offering physical insight in regimes of many-body dynamics, strong coupling, and pulses of finite duration. As there is no requirement for resonant driving, the proposed spectroscopic approach permits physical interpretation of striking, but overlooked, coherence decay features in terms of the form of the avoided crossings of the underlying quasienergy eigenspectrum. This is exemplified by a set of “diamond-shaped” features arising for transverse-field scans in the case of single-spin sensing by nitrogen-vacancy centers in diamond. We also investigate applications for donors in silicon, showing that the resulting tunable interaction strengths offer highly promising future sensors.

  3. Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

    Science.gov (United States)

    Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

  4. Effect of slip on vortex dynamics and forcing of a superhydrophobic cylinder

    Science.gov (United States)

    Muralidhar, Pranesh; Daniello, Robert; Ferrer, Nangelie; Rothstein, Jonathan

    2011-11-01

    Superhydrophobic surfaces have been shown to produce significant drag reduction for both laminar and turbulent flows of water through large and small-scale channels. In this presentation, a series of experiments will be presented which investigate the effect of superhydrophobic-induced slip on the vortex dynamics in the wake of a cylinder and the change in the drag and lift forces thereof. In these experiments, circular cylinders are coated with a series of superhydrophobic surfaces fabricated from PDMS with well-defined micron-sized patterns of surface roughness. Using force measurements and PIV (Particle Image Velocimetry), we will show that these surfaces have a noticeable effect on the drag/lift and vortex dynamics of cylinders. When compared to a smooth, no-slip cylinder, we will show that the lift/drag and the amount of raw vorticity that is shed in the wake of the superhydrophobic cylinder decreases. In addition, we will show that the forcing is sensitive to changes of feature spacing, size and orientation.

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

    Science.gov (United States)

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

    2015-05-07

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

  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. A Piezoelectric PZT Ceramic Mulitlayer Stack for Energy Harvesting Under Dynamic Forces

    Science.gov (United States)

    Xu, Tian-Bing; Siochi, Emilie J.; Kang, Jin Ho; Zuo, Lei; Zhou, Wanlu; Tang, Xiudong; Jiang, Xiaoning

    2011-01-01

    Piezoelectric energy harvesting transducers (PEHTs) are commonly used in motion/vibration energy scavenging devices. To date, most researchers have focused on energy harvesting at narrow bandwidths around the mechanical resonance frequency, and most piezoelectric harvesting devices reported in the literature have very low effective piezoelectric coefficient (d(sub eff)) (coefficients of about 100 pC/N. The level of harvested electrical power for CBPEHTs is on the order of microW even at resonance mode. In order to harvest more electrical energy across broader bandwidth, high effective piezoelectric coefficient structures are needed. In this study, we investigate a "33" longitudinal mode, piezoelectric PZT ceramic multilayer stack (PZT-Stack) with high effective piezoelectric coefficient for high-performance PEHTs. The PZT-Stack is composed of 300 layers of 0.1 mm thick PZT plates, with overall dimensions of 32.4 mm X 7.0 mm X 7.0 mm. Experiments were carried out with dynamic forces in a broad bandwidth ranging from 0.5 Hz to 25 kHz. The measured results show that the effective piezoelectric coefficient of the PZT-stack is about 1 X 10(exp 5) pC/N at off-resonance frequencies and 1.39 X 10(exp 6) pC/N at resonance, which is order of magnitude larger than that of traditional PEHTs. The effective piezoelectric coefficients (d(sub eff)) do not change significantly with applied dynamic forces having root mean square (RMS) values ranging from 1 N to 40 N. In resonance mode, 231 mW of electrical power was harvested at 2479 Hz with a dynamic force of 11.6 N(sub rms), and 7.6 mW of electrical power was generated at a frequency of 2114 Hz with 1 N(sub rms) dynamic force. In off-resonance mode, an electrical power of 18.7 mW was obtained at 680 Hz with a 40 N(sub rms) dynamic force. A theoretical model of energy harvesting for the PZT-Stack is established. The modeled results matched well with experimental measurements. This study demonstrated that high effective

  8. Massively Parallel Single-Molecule Manipulation Using Centrifugal Force

    Science.gov (United States)

    Wong, Wesley; Halvorsen, Ken

    2011-03-01

    Precise manipulation of single molecules has led to remarkable insights in physics, chemistry, biology, and medicine. However, two issues that have impeded the widespread adoption of these techniques are equipment cost and the laborious nature of making measurements one molecule at a time. To meet these challenges, we have developed an approach that enables massively parallel single- molecule force measurements using centrifugal force. This approach is realized in the centrifuge force microscope, an instrument in which objects in an orbiting sample are subjected to a calibration-free, macroscopically uniform force- field while their micro-to-nanoscopic motions are observed. We demonstrate high- throughput single-molecule force spectroscopy with this technique by performing thousands of rupture experiments in parallel, characterizing force-dependent unbinding kinetics of an antibody-antigen pair in minutes rather than days. Currently, we are taking steps to integrate high-resolution detection, fluorescence, temperature control and a greater dynamic range in force. With significant benefits in efficiency, cost, simplicity, and versatility, single-molecule centrifugation has the potential to expand single-molecule experimentation to a wider range of researchers and experimental systems.

  9. Phase-resolved fluid dynamic forces of a flapping foil energy harvester based on PIV measurements

    Science.gov (United States)

    Liburdy, James

    2017-11-01

    Two-dimensional particle image velocimetry measurements are performed in a wind tunnel to evaluate the spatial and temporal fluid dynamic forces acting on a flapping foil operating in the energy harvesting regime. Experiments are conducted at reduced frequencies (k = fc/U) of 0.05 - 0.2, pitching angle of, and heaving amplitude of A / c = 0.6. The phase-averaged pressure field is obtained by integrating the pressure Poisson equation. Fluid dynamic forces are then obtained through the integral momentum equation. Results are compared with a simple force model based on the concept of flow impulse. These results help to show the detailed force distributions, their transient nature and aide in understanding the impact of the fluid flow structures that contribute to the power production.

  10. Ultra-short laser pulse ablation using shear-force feedback: Femtosecond laser induced breakdown spectroscopy feasibility study

    International Nuclear Information System (INIS)

    Samek, Ota; Kurowski, Andre; Kittel, Silke; Kukhlevsky, Sergei; Hergenroeder, Roland

    2005-01-01

    This work reports on a feasibility study of proximity ablation using femtosecond pulses. Ultra-short pulses were launched to a bare tapered optical fiber and delivered to the sample. The tip-sample distance was controlled by means of shear-force feedback. Consequently, ablation craters with submicrometer dimensions were obtained. Potential analytical applications for Laser Induced Breakdown Spectroscopy (LIBS) technique, such as e.g. inclusions in steel or bio cells, are suggested

  11. Dynamic force profile in hydraulic hybrid vehicles: a numerical investigation

    Science.gov (United States)

    Mohaghegh-Motlagh, Amin; Elahinia, Mohammad H.

    2010-04-01

    A hybrid hydraulic vehicle (HHV) combines a hydraulic sub-system with the conventional drivetrain in order to improve fuel economy for heavy vehicles. The added hydraulic module manages the storage and release of fluid power necessary to assist the motion of the vehicle. The power collected by a pump/motor (P/M) from the regenerative braking phase is stored in a high-pressure accumulator and then released by the P/M to the driveshaft during the acceleration phase. This technology is effective in significantly improving fuel-economy for heavy-class vehicles with frequent stop-and-go drive schedules. Despite improved fuel economy and higher vehicle acceleration, noise and vibrations are one of the main problems of these vehicles. The dual function P/Ms are the main source of noise and vibration in a HHV. This study investigates the dynamics of a P/M and particularly the profile and frequency-dependence of the dynamic forces generated by a bent-axis P/M unit. To this end, the fluid dynamics side of the problem has been simplified for investigating the system from a dynamics perspective. A mathematical model of a bent axis P/M has been developed to investigate the cause of vibration and noise in HHVs. The forces are calculated in time and frequency domains. The results of this work can be used to study the vibration response of the chassis and to design effective vibration isolation systems for HHVs.

  12. Low Dose X-Ray Speckle Visibility Spectroscopy Reveals Nanoscale Dynamics in Radiation Sensitive Ionic Liquids

    Science.gov (United States)

    Verwohlt, Jan; Reiser, Mario; Randolph, Lisa; Matic, Aleksandar; Medina, Luis Aguilera; Madsen, Anders; Sprung, Michael; Zozulya, Alexey; Gutt, Christian

    2018-04-01

    X-ray radiation damage provides a serious bottleneck for investigating microsecond to second dynamics on nanometer length scales employing x-ray photon correlation spectroscopy. This limitation hinders the investigation of real time dynamics in most soft matter and biological materials which can tolerate only x-ray doses of kGy and below. Here, we show that this bottleneck can be overcome by low dose x-ray speckle visibility spectroscopy. Employing x-ray doses of 22-438 kGy and analyzing the sparse speckle pattern of count rates as low as 6.7 ×10-3 per pixel, we follow the slow nanoscale dynamics of an ionic liquid (IL) at the glass transition. At the prepeak of nanoscale order in the IL, we observe complex dynamics upon approaching the glass transition temperature TG with a freezing in of the alpha relaxation and a multitude of millisecond local relaxations existing well below TG . We identify this fast relaxation as being responsible for the increasing development of nanoscale order observed in ILs at temperatures below TG .

  13. Dynamic tunneling force microscopy for characterizing electronic trap states in non-conductive surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Wang, R.; Williams, C. C., E-mail: clayton@physics.utah.edu [Department of Physics and Astronomy, University of Utah, Salt Lake City, Utah 84112 (United States)

    2015-09-15

    Dynamic tunneling force microscopy (DTFM) is a scanning probe technique for real space mapping and characterization of individual electronic trap states in non-conductive films with atomic scale spatial resolution. The method is based upon the quantum mechanical tunneling of a single electron back and forth between a metallic atomic force microscopy tip and individual trap states in completely non-conducting surface. This single electron shuttling is measured by detecting the electrostatic force induced on the probe tip at the shuttling frequency. In this paper, the physical basis for the DTFM method is unfolded through a physical model and a derivation of the dynamic tunneling signal as a function of several experimental parameters is shown. Experimental data are compared with the theoretical simulations, showing quantitative consistency and verifying the physical model used. The experimental system is described and representative imaging results are shown.

  14. Collective coordinates and an accompanying metric force in structural isomerization dynamics of molecules

    International Nuclear Information System (INIS)

    Yanao, Tomohiro; Takatsuka, Kazuo

    2003-01-01

    Structural isomerization dynamics of three- and four-atom clusters of vanishing total angular momentum is studied in terms of internal coordinates of n-body systems on the basis of a gauge theory. The so-called principal-axis hyperspherical coordinates are employed effectively as collective variables for the study of isomerization reactions. It turns out that the non-Euclidean metric on the internal space gives rise to a force, which works in response to internal motions called the democratic (kinematic) rotations in the internal space. This metric force generally tends to induce an asymmetry in mass balance of a system, and is coupled with the usual potential force to give rise to trapped motions in the vicinity of the transition states of the cluster. This observation provides a different perspective for the so-called recrossing problem in chemical reaction dynamics

  15. Rotational coherence spectroscopy at FLASH. Toward dynamic studies in nanosuperfluids

    Energy Technology Data Exchange (ETDEWEB)

    Kickermann, Andreas

    2013-07-15

    The field of molecular physics, which is focusing on molecular motion in the transition states of physical, chemical, and biological changes, is a wide-spread research area. It strives to reveal the structural and functional properties of molecules, the chemical bonds between atoms and the time evolution. Many processes occurring in nature upon electronic excitation proceed on the ultrafast femtosecond timescale and can be triggered by modern ultrashort femtosecond-laser sources under laboratory conditions. In the present thesis pump-probe studies were performed to follow molecular motion using ultrashort light pulses in the nanometer wavelength range provided by an XUV freeelectron laser (FEL). In detail, alignment of molecular species in space under field-free conditions was investigated. In the specific case of rotational wave packets in molecules the rotational dynamics shows characteristic temporal features, which contain a wealth of information on molecular structure and give insight into molecular coupling mechanisms, i.e. rotational constants and transition frequencies. Within this thesis, Rotational Coherence Spectroscopy (RCS) reveals wave-packet motion observed by subsequent Coulomb explosion of Raman excited carbon monoxide, which results in a time-dependent asymmetry of spatial fragmentation patterns. With the method presented here, the time resolution to elucidate the fast dynamics of strong couplings can be pushed toward a single rotational period even for the fastest rotors. This is due to large pump-probe delays with small subpicosecond step size. This kind of spectroscopy can also be expanded to molecular species, which are not accessible by other powerful spectroscopic methods, such as Fourier-transform microwave spectroscopy (FTMW). Furthermore, it allows to measure weak molecular couplings on a long timescale (large pump-probe delays), e.g. couplings of molecules in a solution or molecules dissolved in quantum fluids. This is valuable to

  16. Rotational coherence spectroscopy at FLASH. Toward dynamic studies in nanosuperfluids

    International Nuclear Information System (INIS)

    Kickermann, Andreas

    2013-07-01

    The field of molecular physics, which is focusing on molecular motion in the transition states of physical, chemical, and biological changes, is a wide-spread research area. It strives to reveal the structural and functional properties of molecules, the chemical bonds between atoms and the time evolution. Many processes occurring in nature upon electronic excitation proceed on the ultrafast femtosecond timescale and can be triggered by modern ultrashort femtosecond-laser sources under laboratory conditions. In the present thesis pump-probe studies were performed to follow molecular motion using ultrashort light pulses in the nanometer wavelength range provided by an XUV freeelectron laser (FEL). In detail, alignment of molecular species in space under field-free conditions was investigated. In the specific case of rotational wave packets in molecules the rotational dynamics shows characteristic temporal features, which contain a wealth of information on molecular structure and give insight into molecular coupling mechanisms, i.e. rotational constants and transition frequencies. Within this thesis, Rotational Coherence Spectroscopy (RCS) reveals wave-packet motion observed by subsequent Coulomb explosion of Raman excited carbon monoxide, which results in a time-dependent asymmetry of spatial fragmentation patterns. With the method presented here, the time resolution to elucidate the fast dynamics of strong couplings can be pushed toward a single rotational period even for the fastest rotors. This is due to large pump-probe delays with small subpicosecond step size. This kind of spectroscopy can also be expanded to molecular species, which are not accessible by other powerful spectroscopic methods, such as Fourier-transform microwave spectroscopy (FTMW). Furthermore, it allows to measure weak molecular couplings on a long timescale (large pump-probe delays), e.g. couplings of molecules in a solution or molecules dissolved in quantum fluids. This is valuable to

  17. Multipolar Force Fields and Their Effects on Solvent Dynamics around Simple Solutes

    DEFF Research Database (Denmark)

    Jakobsen, Sofie; Bereau, Tristan; Meuwly, Markus

    2015-01-01

    The performance of multipole (MTP) and point charge (PC) force fields in classical molecular dynamics (MD) simulations of condensed-phase systems for both equilibrium and dynamical quantities is compared. MTP electrostatics provides an improved description of the anisotropic electrostatic potential......, which is especially important to describe key, challenging interactions, such as lone pairs, π-interactions, and hydrogen bonds. These chemical environments are probed by focusing on the hydration properties of two molecules: N-methylacetamide and phenyl bromide. Both, equilibrium and dynamical...

  18. Time-resolved X-ray photoelectron spectroscopy techniques for the study of interfacial charge dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Neppl, Stefan, E-mail: sneppl@lbl.gov; Gessner, Oliver

    2015-04-15

    Highlights: • Ultrafast interfacial charge transfer is probed with atomic site specificity. • Femtosecond X-ray photoelectron spectroscopy using a free electron laser. • Efficient and flexible picosecond X-ray photoelectron pump–probe scheme using synchrotron radiation. - Abstract: X-ray photoelectron spectroscopy (XPS) is one of the most powerful techniques to quantitatively analyze the chemical composition and electronic structure of surfaces and interfaces in a non-destructive fashion. Extending this technique into the time domain has the exciting potential to shed new light on electronic and chemical dynamics at surfaces by revealing transient charge configurations with element- and site-specificity. Here, we describe prospects and challenges that are associated with the implementation of picosecond and femtosecond time-resolved X-ray photoelectron spectroscopy at third-generation synchrotrons and X-ray free-electron lasers, respectively. In particular, we discuss a series of laser-pump/X-ray-probe photoemission experiments performed on semiconductor surfaces, molecule-semiconductor interfaces, and films of semiconductor nanoparticles that demonstrate the high sensitivity of time-resolved XPS to light-induced charge carrier generation, diffusion and recombination within the space charge layers of these materials. Employing the showcase example of photo-induced electronic dynamics in a dye-sensitized semiconductor system, we highlight the unique possibility to probe heterogeneous charge transfer dynamics from both sides of an interface, i.e., from the perspective of the molecular electron donor and the semiconductor acceptor, simultaneously. Such capabilities will be crucial to improve our microscopic understanding of interfacial charge redistribution and associated chemical dynamics, which are at the heart of emerging energy conversion, solar fuel generation, and energy storage technologies.

  19. Magnetohydrodynamic Modeling of Solar Coronal Dynamics with an Initial Non-force-free Magnetic Field

    Energy Technology Data Exchange (ETDEWEB)

    Prasad, A.; Bhattacharyya, R.; Kumar, Sanjay [Udaipur Solar Observatory, Physical Research Laboratory, Dewali, Bari Road, Udaipur-313001 (India)

    2017-05-01

    The magnetic fields in the solar corona are generally neither force-free nor axisymmetric and have complex dynamics that are difficult to characterize. Here we simulate the topological evolution of solar coronal magnetic field lines (MFLs) using a magnetohydrodynamic model. The simulation is initialized with a non-axisymmetric non-force-free magnetic field that best correlates with the observed vector magnetograms of solar active regions (ARs). To focus on these ideas, simulations are performed for the flaring AR 11283 noted for its complexity and well-documented dynamics. The simulated dynamics develops as the initial Lorentz force pushes the plasma and facilitates successive magnetic reconnections at the two X-type null lines present in the initial field. Importantly, the simulation allows for the spontaneous development of mass flow, unique among contemporary works, that preferentially reconnects field lines at one of the X-type null lines. Consequently, a flux rope consisting of low-lying twisted MFLs, which approximately traces the major polarity inversion line, undergoes an asymmetric monotonic rise. The rise is attributed to a reduction in the magnetic tension force at the region overlying the rope, resulting from the reconnection. A monotonic rise of the rope is in conformity with the standard scenario of flares. Importantly, the simulated dynamics leads to bifurcations of the flux rope, which, being akin to the observed filament bifurcation in AR 11283, establishes the appropriateness of the initial field in describing ARs.

  20. Spin motive force driven by the magnetization dynamics in chiral magnets

    International Nuclear Information System (INIS)

    Ohe, Jun-ichiro; Shimada, Yuhki

    2015-01-01

    The magnetization dynamics induces the spin-dependent force on the conduction electrons via the s-d coupling. We have investigated numerically this force, so called 'spin-motive force', generated in chiral magnets forming the Skyrmion structure. We solve the Landau-Lifshitz-Gilbert equation and obtain the Skyrmion lattice structure (SkX) by introducing the Dzyaloshinskii-Moriya (DM) interaction. The corrective mode of the Skyrmion core is obtained by applying the in-plane AC magnetic field. The spin-motive force is generated perpendicular to the velocity of the Skyrmion core. The total voltage due to the spin-motive force is enhanced by the cascade effect of the voltage for each Skyrmion core. For the isolated magnetic disc system, the corrective mode of the Skyrmion lattice is modulated from that of the bulk system by the influence of the edge structure. The phase-locking motion of each Skyrmion core is obtained only in the lowest frequency mode in which the cascade effect of the spin-motive force still remain. (author)

  1. Multidimensional high harmonic spectroscopy

    International Nuclear Information System (INIS)

    Bruner, Barry D; Soifer, Hadas; Shafir, Dror; Dudovich, Nirit; Serbinenko, Valeria; Smirnova, Olga

    2015-01-01

    High harmonic generation (HHG) has opened up a new frontier in ultrafast science where attosecond time resolution and Angstrom spatial resolution are accessible in a single measurement. However, reconstructing the dynamics under study is limited by the multiple degrees of freedom involved in strong field interactions. In this paper we describe a new class of measurement schemes for resolving attosecond dynamics, integrating perturbative nonlinear optics with strong-field physics. These approaches serve as a basis for multidimensional high harmonic spectroscopy. Specifically, we show that multidimensional high harmonic spectroscopy can measure tunnel ionization dynamics with high precision, and resolves the interference between multiple ionization channels. In addition, we show how multidimensional HHG can function as a type of lock-in amplifier measurement. Similar to multi-dimensional approaches in nonlinear optical spectroscopy that have resolved correlated femtosecond dynamics, multi-dimensional high harmonic spectroscopy reveals the underlying complex dynamics behind attosecond scale phenomena. (paper)

  2. Quantum dynamics and electronic spectroscopy within the framework of wavelets

    International Nuclear Information System (INIS)

    Toutounji, Mohamad

    2013-01-01

    This paper serves as a first-time report on formulating important aspects of electronic spectroscopy and quantum dynamics in condensed harmonic systems using the framework of wavelets, and a stepping stone to our future work on developing anharmonic wavelets. The Morlet wavelet is taken to be the mother wavelet for the initial state of the system of interest. This work reports daughter wavelets that may be used to study spectroscopy and dynamics of harmonic systems. These wavelets are shown to arise naturally upon optical electronic transition of the system of interest. Natural birth of basis (daughter) wavelets emerging on exciting an electronic two-level system coupled, both linearly and quadratically, to harmonic phonons is discussed. It is shown that this takes place through using the unitary dilation and translation operators, which happen to be part of the time evolution operator of the final electronic state. The corresponding optical autocorrelation function and linear absorption spectra are calculated to test the applicability and correctness of the herein results. The link between basis wavelets and the Liouville space generating function is established. An anharmonic mother wavelet is also proposed in the case of anharmonic electron–phonon coupling. A brief description of deriving anharmonic wavelets and the corresponding anharmonic Liouville space generating function is explored. In conclusion, a mother wavelet (be it harmonic or anharmonic) which accounts for Duschinsky mixing is suggested. (paper)

  3. Observing Solvation Dynamics with Simultaneous Femtosecond X-ray Emission Spectroscopy and X-ray Scattering

    DEFF Research Database (Denmark)

    Haldrup, Kristoffer; Gawelda, Wojciech; Abela, Rafael

    2016-01-01

    and structural changes, and local solvent structural changes are desired. We have studied the intra- and intermolecular dynamics of a model chromophore, aqueous [Fe(bpy)3]2+, with complementary X-ray tools in a single experiment exploiting intense XFEL radiation as a probe. We monitored the ultrafast structural...... rearrangement of the solute with X-ray emission spectroscopy, thus establishing time zero for the ensuing X-ray diffuse scattering analysis. The simultaneously recorded X-ray diffuse scattering atterns reveal slower subpicosecond dynamics triggered by the intramolecular structural dynamics of the photoexcited...

  4. α-Helix Unwinding as Force Buffer in Spectrins.

    Science.gov (United States)

    Takahashi, Hirohide; Rico, Felix; Chipot, Christophe; Scheuring, Simon

    2018-03-27

    Spectrins are cytoskeletal proteins located at the inner face of the plasma membrane, making connections between membrane anchors and the actin cortex, and between actin filaments. Spectrins share a common structure forming a bundle of 3 α-helices and play a major role during cell deformation. Here, we used high-speed force spectroscopy and steered molecular dynamics simulations to understand the mechanical stability of spectrin, revealing a molecular force buffering function. We find that spectrin acts as a soft spring at short extensions (70-100 Å). Under continuous external stretching, its α-helices unwind, leading to a viscous mechanical response over larger extensions (100-300 Å), represented by a constant-force plateau in force/extension curves. This viscous force buffering emerges from a quasi-equilibrium competition between disruption and re-formation of α-helical hydrogen bonds. Our results suggest that, in contrast to β-sheet proteins, which unfold in a catastrophic event, α-helical spectrins dominantly unwind, providing a viscous force buffer over extensions about 5 times their folded length.

  5. Polyphilic Interactions as Structural Driving Force Investigated by Molecular Dynamics Simulation (Project 7

    Directory of Open Access Journals (Sweden)

    Christopher Peschel

    2017-09-01

    Full Text Available We investigated the effect of fluorinated molecules on dipalmitoylphosphatidylcholine (DPPC bilayers by force-field molecular dynamics simulations. In the first step, we developed all-atom force-field parameters for additive molecules in membranes to enable an accurate description of those systems. On the basis of this force field, we performed extensive simulations of various bilayer systems containing different additives. The additive molecules were chosen to be of different size and shape, and they included small molecules such as perfluorinated alcohols, but also more complex molecules. From these simulations, we investigated the structural and dynamic effects of the additives on the membrane properties, as well as the behavior of the additive molecules themselves. Our results are in good agreement with other theoretical and experimental studies, and they contribute to a microscopic understanding of interactions, which might be used to specifically tune membrane properties by additives in the future.

  6. Molecular Dynamics Simulations of a Linear Nanomotor Driven by Thermophoretic Forces

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.

    Molecular Dynamics of a Linear Nanomotor Driven by Thermophoresis Harvey A. Zambrano1, Jens H. Walther1,2 and Richard L. Jaffe3 1Department of Mechanical Engineering, Fluid Mechanics, Technical University of Denmark, DK-2800 Lyngby, Denmark; 2Computational Science and Engineering Laboratory, ETH...... future molecular machines a complete understanding of the friction forces involved on the transport process at the molecular level have to be addressed.18 In this work we perform Molecular Dynamics (MD) simulations using the MD package FASTTUBE19 to study a molecular linear motor consisting of coaxial...... the valence forces within the CNT using Morse, harmonic angle and torsion potentials.19We include a nonbonded carbon-carbon Lennard-Jones potential to describe the vdW interaction between the carbon atoms within the double wall portion of the system. We equilibrate the system at 300K for 0.1 ns, by coupling...

  7. Binaries traveling through a gaseous medium: dynamical drag forces and internal torques

    Energy Technology Data Exchange (ETDEWEB)

    Sánchez-Salcedo, F. J. [Instituto de Astronomía, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apt. Postal 70 264, C.P. 04510, Mexico City (Mexico); Chametla, Raul O., E-mail: jsanchez@astro.unam.mx [Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, UP Adolfo López Mateos, Mexico City (Mexico)

    2014-10-20

    Using time-dependent linear theory, we investigate the morphology of the gravitational wake induced by a binary, whose center of mass moves at velocity V{sub cm} against a uniform background of gas. For simplicity, we assume that the components of the binary are on circular orbits about their common center of mass. The consequences of dynamical friction is twofold. First, gas dynamical friction may drag the center of mass of the binary and cause the binary to migrate. Second, drag forces also induce a braking torque, which causes the orbits of the components of the binary to shrink. We compute the drag forces acting on one component of the binary due to the gravitational interaction with its own wake. We show that the dynamical friction force responsible for decelerating the center of mass of the binary is smaller than it is in the point-mass case because of the loss of gravitational focusing. We show that the braking internal torque depends on the Mach numbers of each binary component about their center of mass, and also on the Mach number of the center of mass of the binary. In general, the internal torque decreases with increasing the velocity of the binary relative to the ambient gas cloud. However, this is not always the case. We also mention the relevance of our results to the period distribution of binaries.

  8. Identification of Random Dynamic Force Using an Improved Maximum Entropy Regularization Combined with a Novel Conjugate Gradient

    Directory of Open Access Journals (Sweden)

    ChunPing Ren

    2017-01-01

    Full Text Available We propose a novel mathematical algorithm to offer a solution for the inverse random dynamic force identification in practical engineering. Dealing with the random dynamic force identification problem using the proposed algorithm, an improved maximum entropy (IME regularization technique is transformed into an unconstrained optimization problem, and a novel conjugate gradient (NCG method was applied to solve the objective function, which was abbreviated as IME-NCG algorithm. The result of IME-NCG algorithm is compared with that of ME, ME-CG, ME-NCG, and IME-CG algorithm; it is found that IME-NCG algorithm is available for identifying the random dynamic force due to smaller root mean-square-error (RMSE, lower restoration time, and fewer iterative steps. Example of engineering application shows that L-curve method is introduced which is better than Generalized Cross Validation (GCV method and is applied to select regularization parameter; thus the proposed algorithm can be helpful to alleviate the ill-conditioned problem in identification of dynamic force and to acquire an optimal solution of inverse problem in practical engineering.

  9. Relaxations and fast dynamics of the plastic crystal cyclo-octanol investigated by broadband dielectric spectroscopy

    OpenAIRE

    Lunkenheimer, Peter

    1997-01-01

    Relaxations and fast dynamics of the plastic crystal cyclo-octanol investigated by broadband dielectric spectroscopy / R. Brand, P. Lunkenheimer, A. Loidl. - In: Physical review. B. 56. 1997. S. R5713-R5716

  10. Bubble dynamics in microchannels: inertial and capillary migration forces

    Science.gov (United States)

    Rivero-Rodriguez, Javier; Scheid, Benoit

    2018-05-01

    This work focuses on the dynamics of a train of unconfined bubbles flowing in microchan- nels. We investigate the transverse position of a train of bubbles, its velocity and the associated pressure drop when flowing in a microchannel depending on the internal forces due to viscosity, inertia and capillarity. Despite the small scales of the system, inertia, referred to as inertial migration force, play a crucial role in determining the transverse equilibrium position of the bubbles. Beside inertia and viscosity, other effects may also affect the transverse migration of bubbles such as the Marangoni surface stresses and the surface deformability. We look at the influence of surfactants in the limit of infinite Marangoni effect which yields rigid bubble interface. The resulting migration force may balance external body forces if present such as buoyancy, Dean or magnetic ones. This balance not only determines the transverse position of the bubbles but, consequently, the surrounding flow structure, which can be determinant for any mass/heat transfer process involved. Finally, we look at the influence of the bubble deformation on the equilibrium position and compare it to the inertial migration force at the centred position, explaining the stable or unstable character of this position accordingly. A systematic study of the influence of the parameters - such as the bubble size, uniform body force, Reynolds and capillary numbers - has been carried out using numerical simulations based on the Finite Element Method, solving the full steady Navier-Stokes equations and its asymptotic counterpart for the limits of small Reynolds and/or capillary numbers.

  11. A modified social force model for crowd dynamics

    Science.gov (United States)

    Hassan, Ummi Nurmasyitah; Zainuddin, Zarita; Abu-Sulyman, Ibtesam M.

    2017-08-01

    The Social Force Model (SFM) is one of the most successful models in microscopic pedestrian studies that is used to study the movement of pedestrians. Many modifications have been done to improvise the SFM by earlier researchers such as the incorporation of a constant respect factor into the self-stopping mechanism. Before the new mechanism is introduced, the researchers found out that a pedestrian will immediately come to a halt if other pedestrians are near to him, which seems to be an unrealistic behavior. Therefore, researchers introduce a self-slowing mechanism to gradually stop a pedestrian when he is approaching other pedestrians. Subsequently, the dynamic respect factor is introduced into the self-slowing mechanism based on the density of the pedestrians to make the model even more realistic. In real life situations, the respect factor of the pedestrians should be dynamic values instead of a constant value. However, when we reproduce the simulation of the dynamic respect factor, we found that the movement of the pedestrians are unrealistic because the pedestrians are lacking perception of the pedestrians in front of him. In this paper, we adopted both dynamic respect factor and dynamic angular parameter, called modified dynamic respect factor, which is dependent on the density of the pedestrians. Simulations are performed in a normal unidirectional walkway to compare the simulated pedestrians' movements produced by both models. The results obtained showed that the modified dynamic respect factor produces more realistic movement of the pedestrians which conform to the real situation. Moreover, we also found that the simulations endow the pedestrian with a self-slowing mechanism and a perception of other pedestrians in front of him.

  12. 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.

  13. 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

  14. Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions

    Energy Technology Data Exchange (ETDEWEB)

    Bradforth, Stephen Edmund [Univ. of California, Berkeley, CA (United States)

    1992-11-01

    The transition state region of a neutral bimolecular reaction may be experimentally investigated by photoelectron spectroscopy of an appropriate negative ion. The photoelectron spectrum provides information on the spectroscopy and dynamics of the short lived transition state and may be used to develop model potential energy surfaces that are semi-quantitative in this important region. The principles of bound {yields} bound negative ion photoelectron spectroscopy are illustrated by way of an example: a full analysis of the photoelectron bands of CN-, NCO- and NCS-. Transition state photoelectron spectra are presented for the following systems Br + HI, Cl + HI, F + HI, F + CH30H,F + C2H5OH,F + OH and F + H2. A time dependent framework for the simulation and interpretation of the bound → free transition state photoelectron spectra is subsequently developed and applied to the hydrogen transfer reactions Br + HI, F + OH → O(3P, 1D) + HF and F + H2. The theoretical approach for the simulations is a fully quantum-mechanical wave packet propagation on a collinear model reaction potential surface. The connection between the wavepacket time evolution and the photoelectron spectrum is given by the time autocorrelation function. For the benchmark F + H2 system, comparisons with three-dimensional quantum calculations are made.

  15. Clocking Femtosecond Collisional Dynamics via Resonant X-Ray Spectroscopy

    Science.gov (United States)

    van den Berg, Q. Y.; Fernandez-Tello, E. V.; Burian, T.; Chalupský, J.; Chung, H.-K.; Ciricosta, O.; Dakovski, G. L.; Hájková, V.; Hollebon, P.; Juha, L.; Krzywinski, J.; Lee, R. W.; Minitti, M. P.; Preston, T. R.; de la Varga, A. G.; Vozda, V.; Zastrau, U.; Wark, J. S.; Velarde, P.; Vinko, S. M.

    2018-02-01

    Electron-ion collisional dynamics is of fundamental importance in determining plasma transport properties, nonequilibrium plasma evolution, and electron damage in diffraction imaging applications using bright x-ray free-electron lasers (FELs). Here we describe the first experimental measurements of ultrafast electron impact collisional ionization dynamics using resonant core-hole spectroscopy in a solid-density magnesium plasma, created and diagnosed with the Linac Coherent Light Source x-ray FEL. By resonantly pumping the 1 s →2 p transition in highly charged ions within an optically thin plasma, we have measured how off-resonance charge states are populated via collisional processes on femtosecond time scales. We present a collisional cross section model that matches our results and demonstrates how the cross sections are enhanced by dense-plasma effects including continuum lowering. Nonlocal thermodynamic equilibrium collisional radiative simulations show excellent agreement with the experimental results and provide new insight on collisional ionization and three-body-recombination processes in the dense-plasma regime.

  16. Dynamics of Exciton Relaxation in LH2 Antenna Probed by Multipulse Nonlinear Spectroscopy

    NARCIS (Netherlands)

    Novoderezhkin, V.I.; Cohen Stuart, T.A.; van Grondelle, R.

    2011-01-01

    We explain the relaxation dynamics in the LH2-B850 antenna as revealed by multipulse pump - dump - probe spectroscopy (Th. A. Cohen StuartM. VengrisV. I. NovoderezhkinR. J. CogdellC. N. HunterR. van Grondelle, submitted). The theory of pump - dump - probe response is evaluated using the doorway -

  17. Mechanisms of ultrafast fluorescence depletion spectroscopy and applications to measure slovation dynamics of coummarin 153 in methanol

    International Nuclear Information System (INIS)

    Yang Songqiu; Liu Jianyong; Zhou Panwang; Chen Junsheng; Han Keli; He Guozhong

    2012-01-01

    Subpicosecond fluorescence depletion spectroscopy (FDS) was used to measure the solvation dynamics of coumarin 153 (C153) in methanol. The FDS mechanisms were discussed. A quasi-continuous model was used to describe the solvational relaxation of excited states. The perturbations of the probe pulse on the excited sample system, including up-conversion and stimulated emission, were sufficiently discussed. For a probe molecule used in the FDS experiment, ensuring that the up-conversion perturbation can be negligible is important. FDS was found to be a good technique for measuring the solvation dynamics of C153 in methanol. - Highlights: ► Mechanisms of subpicosecond fluorescence depletion spectroscopy. ► Quasi-continuous model was used to describe the solvational relaxation. ► The solvation dynamics of coumarin 153 in methanol has been measured.

  18. Constant Cutting Force Control for CNC Machining Using Dynamic Characteristic-Based Fuzzy Controller

    Directory of Open Access Journals (Sweden)

    Hengli Liu

    2015-01-01

    Full Text Available This paper presents a dynamic characteristic-based fuzzy adaptive control algorithm (DCbFACA to avoid the influence of cutting force changing rapidly on the machining stability and precision. The cutting force is indirectly obtained in real time by monitoring and extraction of the motorized spindle current, the feed speed is fuzzy adjusted online, and the current was used as a feedback to control cutting force and maintain the machining process stable. Different from the traditional fuzzy control methods using the experience-based control rules, and according to the complex nonlinear characteristics of CNC machining, the power bond graph method is implemented to describe the dynamic characteristics of process, and then the appropriate variation relations are achieved between current and feed speed, and the control rules are optimized and established based on it. The numerical results indicated that DCbFACA can make the CNC machining process more stable and improve the machining precision.

  19. Resolving dual binding conformations of cellulosome cohesin-dockerin complexes using single-molecule force spectroscopy.

    Science.gov (United States)

    Jobst, Markus A; Milles, Lukas F; Schoeler, Constantin; Ott, Wolfgang; Fried, Daniel B; Bayer, Edward A; Gaub, Hermann E; Nash, Michael A

    2015-10-31

    Receptor-ligand pairs are ordinarily thought to interact through a lock and key mechanism, where a unique molecular conformation is formed upon binding. Contrary to this paradigm, cellulosomal cohesin-dockerin (Coh-Doc) pairs are believed to interact through redundant dual binding modes consisting of two distinct conformations. Here, we combined site-directed mutagenesis and single-molecule force spectroscopy (SMFS) to study the unbinding of Coh:Doc complexes under force. We designed Doc mutations to knock out each binding mode, and compared their single-molecule unfolding patterns as they were dissociated from Coh using an atomic force microscope (AFM) cantilever. Although average bulk measurements were unable to resolve the differences in Doc binding modes due to the similarity of the interactions, with a single-molecule method we were able to discriminate the two modes based on distinct differences in their mechanical properties. We conclude that under native conditions wild-type Doc from Clostridium thermocellum exocellulase Cel48S populates both binding modes with similar probabilities. Given the vast number of Doc domains with predicted dual binding modes across multiple bacterial species, our approach opens up new possibilities for understanding assembly and catalytic properties of a broad range of multi-enzyme complexes.

  20. Social Forces Sustaining the Israeli-Palestinian Tensions: A Dynamical Psychology Perspective

    Directory of Open Access Journals (Sweden)

    Jay Lawrence Michaels

    2017-07-01

    Full Text Available The Israeli-Palestinian conflict remains one of the most deeply entrenched in the world. While there is great knowledge about numerous individual factors contributing to this conflict’s persistence, much of the information is fragmented and segregated into different disciplines. This article seeks to integrate an array of literature using a dynamic systems perspective to examine how social – as opposed to political – forces contribute to ongoing tensions. The first part describes the dynamical systems perspective, focusing on how intractable conflicts emerge as a result of interlinking factors that anchor the social system in patterns that resist change. The second part explores the Israeli-Palestinian conflict in terms of specific social forces contributing to the conflict’s persistence. These include leadership issues, economic inequalities poverty, youth disenfranchisement, and population distribution. Then the contribution maps how the discussed social factors interrelate to reinforce the ongoing tensions and addresses how small-scale approaches may circumvent the volatile, entrenched patterns of hostility.

  1. Time dependence of the natural passivation process on AISI 304 in an alkaline medium: Atomic force microscopy and scanning Kelvin probe force microscopy as additional tools to electrochemical impedance spectroscopy

    Science.gov (United States)

    Benaioun, N. E.; Maafa, I.; Florentin, A.; Denys, E.; Hakiki, N. E.; Moulayat, N.; Bubendorff, J. L.

    2018-04-01

    Thin surface films formed on AISI 304 samples in an alkaline solution of pH = 13 are studied by atomic force microscopy (AFM), scanning Kelvin probe force microscopy (SKPFM) and electrochemical impedance spectroscopy (EIS) as a function of immersion time. The results reveal that changes on EIS diagrams correspond to topographical modifications on the sample surface as shown by AFM. Both techniques are therefore complementary. The oxide layer is chemically homogenous as shown by SKPFM imaging and our ultra-thin passive layer is an efficient barrier against corrosion.

  2. Complex dynamics in Duffing system with two external forcings

    International Nuclear Information System (INIS)

    Jing Zhujun; Wang Ruiqi

    2005-01-01

    Duffing's equation with two external forcing terms have been discussed. The threshold values of chaotic motion under the periodic and quasi-periodic perturbations are obtained by using second-order averaging method and Melnikov's method. Numerical simulations not only show the consistence with the theoretical analysis but also exhibit the interesting bifurcation diagrams and the more new complex dynamical behaviors, including period-n (n=2,3,6,8) orbits, cascades of period-doubling and reverse period doubling bifurcations, quasi-periodic orbit, period windows, bubble from period-one to period-two, onset of chaos, hopping behavior of chaos, transient chaos, chaotic attractors and strange non-chaotic attractor, crisis which depends on the frequencies, amplitudes and damping. In particular, the second frequency plays a very important role for dynamics of the system, and the system can leave chaotic region to periodic motions by adjusting some parameter which can be considered as an control strategy of chaos. The computation of Lyapunov exponents confirm the dynamical behaviors

  3. Dynamic behavior of tuning fork shear-force structures in a SNOM system

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Fengli [Department of Engineering Mechanics, AML, CNMM, Tsinghua University, Beijing 100084 (China); Li, Xide, E-mail: lixide@tsinghua.edu.cn [Department of Engineering Mechanics, AML, CNMM, Tsinghua University, Beijing 100084 (China); Wang, Jia [State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, Beijing 100084 (China); Fu, Yu [Temasek Laboratories, Nanyang Technological University, 50 Nanyang Drive, 637553 (Singapore)

    2014-07-01

    Piezoelectric tuning fork shear-force structures are widely used as a distance control unit in a scanning near-field optical microscopy. However, the complex dynamic behavior among the micro-tuning forks (TFs), optical fiber probes, and the probe–surface interactions is still a crucial issue to achieve high-resolution imaging or near-field interaction inspections. Based on nonlinear beam tension-bending vibration theory, vibration equations in both longitudinal and lateral directions have been established when the TF structure and the optical fiber are treated as deformable structures. The relationship of the probe–surface interaction induced by Van der Waals force has been analyzed and the corresponding numerical results used to describe the vibrational behavior of the probe approaching the sample surface are obtained. Meanwhile, the viscous resistance of the liquid film on the sample surface has also been investigated using linear beam-bending vibration theory. Experiments testing the interaction between the probe and the water film on a single crystal silicon wafer have been carried out and the viscous resistance of the water film was estimated using the established equations. Finally, to use the TF-probe structure as a force sensor, the relation between the dynamic response of the TF-probe system and an external force on the probe tip was obtained. - Highlights: • Nonlinear vibration equation is established for a deformable tuning fork probe assembly. • Probe–sample interactions induced by Van der Waals force and viscous resistance are investigated. • The viscous resistance between the probe and the water film is estimated using testing results.

  4. Nonlinear dynamic analysis of piping systems using the pseudo force method

    International Nuclear Information System (INIS)

    Prachuktam, S.; Bezler, P.; Hartzman, M.

    1979-01-01

    Simple piping systems are composed of linear elastic elements and can be analyzed using conventional linear methods. The introduction of constraint springs separated from the pipe with clearance gaps to such systems to cope with the pipe whip or other extreme excitation conditions introduces nonlinearities to the system, the nonlinearities being associated with the gaps. Since these spring-damper constraints are usually limited in number, descretely located, and produce only weak nonlinearities, the analysis of linear systems including these nonlinearities can be carried out by using modified linear methods. In particular, the application of pseudo force methods wherein the nonlinearities are treated as displacement dependent forcing functions acting on the linear system were investigated. The nonlinearities induced by the constraints are taken into account as generalized pseudo forces on the right-hand side of the governing dynamic equilibrium equations. Then an existing linear elastic finite element piping code, EPIPE, was modified to permit application of the procedure. This option was inserted such that the analyses could be performed using either the direct integration method or via a modal superposition method, the Newmark-Beta integration procedure being employed in both methods. The modified code was proof tested against several problems taken from the literature or developed with the nonlinear dynamics code OSCIL. The problems included a simple pipe loop, cantilever beam, and lumped mass system subjected to pulsed and periodic forcing functions. The problems were selected to gage the overall accuracy of the method and to insure that it properly predicted the jump phenomena associated with nonlinear systems. (orig.)

  5. Free Energy Reconstruction from Logarithmic Mean-Force Dynamics Using Multiple Nonequilibrium Trajectories.

    Science.gov (United States)

    Morishita, Tetsuya; Yonezawa, Yasushige; Ito, Atsushi M

    2017-07-11

    Efficient and reliable estimation of the mean force (MF), the derivatives of the free energy with respect to a set of collective variables (CVs), has been a challenging problem because free energy differences are often computed by integrating the MF. Among various methods for computing free energy differences, logarithmic mean-force dynamics (LogMFD) [ Morishita et al., Phys. Rev. E 2012 , 85 , 066702 ] invokes the conservation law in classical mechanics to integrate the MF, which allows us to estimate the free energy profile along the CVs on-the-fly. Here, we present a method called parallel dynamics, which improves the estimation of the MF by employing multiple replicas of the system and is straightforwardly incorporated in LogMFD or a related method. In the parallel dynamics, the MF is evaluated by a nonequilibrium path-ensemble using the multiple replicas based on the Crooks-Jarzynski nonequilibrium work relation. Thanks to the Crooks relation, realizing full-equilibrium states is no longer mandatory for estimating the MF. Additionally, sampling in the hidden subspace orthogonal to the CV space is highly improved with appropriate weights for each metastable state (if any), which is hardly achievable by typical free energy computational methods. We illustrate how to implement parallel dynamics by combining it with LogMFD, which we call logarithmic parallel dynamics (LogPD). Biosystems of alanine dipeptide and adenylate kinase in explicit water are employed as benchmark systems to which LogPD is applied to demonstrate the effect of multiple replicas on the accuracy and efficiency in estimating the free energy profiles using parallel dynamics.

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

    Science.gov (United States)

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

    2013-04-01

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

  7. Characterization of polymer surface structure and surface mechanical behaviour by sum frequency generation surface vibrational spectroscopy and atomic force microscopy

    International Nuclear Information System (INIS)

    Opdahl, Aric; Koffas, Telly S; Amitay-Sadovsky, Ella; Kim, Joonyeong; Somorjai, Gabor A

    2004-01-01

    Sum frequency generation (SFG) vibrational spectroscopy and atomic force microscopy (AFM) have been used to study polymer surface structure and surface mechanical behaviour, specifically to study the relationships between the surface properties of polymers and their bulk compositions and the environment to which the polymer is exposed. The combination of SFG surface vibrational spectroscopy and AFM has been used to study surface segregation behaviour of polyolefin blends at the polymer/air and polymer/solid interfaces. SFG surface vibrational spectroscopy and AFM experiments have also been performed to characterize the properties of polymer/liquid and polymer/polymer interfaces, focusing on hydrogel materials. A method was developed to study the surface properties of hydrogel contact lens materials at various hydration conditions. Finally, the effect of mechanical stretching on the surface composition and surface mechanical behaviour of phase-separated polyurethanes, used in biomedical implant devices, has been studied by both SFG surface vibrational spectroscopy and AFM. (topical review)

  8. Characterizing interstate vibrational coherent dynamics of surface adsorbed catalysts by fourth-order 3D SFG spectroscopy

    Science.gov (United States)

    Li, Yingmin; Wang, Jiaxi; Clark, Melissa L.; Kubiak, Clifford P.; Xiong, Wei

    2016-04-01

    We report the first fourth-order 3D SFG spectroscopy of a monolayer of the catalyst Re(diCN-bpy)(CO)3Cl on a gold surface. Besides measuring the vibrational coherences of single vibrational modes, the fourth-order 3D SFG spectrum also measures the dynamics of interstate coherences and vibrational coherences states between two vibrational modes. By comparing the 3D SFG to the corresponding 2D and third-order 3D IR spectroscopy of the same molecules in solution, we found that the interstate coherences exist in both liquid and surface systems, suggesting that the interstate coherence is not disrupted by surface interactions. However, by analyzing the 3D spectral lineshape, we found that the interstate coherences also experience non-negligible homogenous dephasing dynamics that originate from surface interactions. This unique ability of determining interstate vibrational coherence dynamics of the molecular monolayer can help in understanding of how energy flows within surface catalysts and other molecular monolayers.

  9. High resolution neutron spectroscopy - a tool for the investigation of dynamics of polymers and soft matter; La spectroscopie de neutrons a haute resolution-un outil pour l'etude de la dynamique des polymeres et de la matiere molle

    Energy Technology Data Exchange (ETDEWEB)

    Monkenbusch, M.; Richter, D. [Institut fur Festkorperforschung (IFF), Forschungszentrum Julich, Julich (Germany)

    2007-09-15

    Neutron scattering, with the ability to vary the contrast of molecular items by hydrogen/deuterium exchanges, is an invaluable tool for soft matter research. Besides the structural information on the mesoscopic scale that is obtained by diffraction methods like small angle neutron scattering, the slow dynamics of molecular motion on mesoscopic scale is accessible by high resolution neutron spectroscopy. The basic features of neutron backscattering spectroscopy, and in particular neutron spin-echo spectroscopy, are presented, in combination with illustrations of results from polymer melt dynamics to protein dynamics which are obtained by these techniques. (authors)

  10. Measurement of Vehicle-Bridge-Interaction force using dynamic tire pressure monitoring

    Science.gov (United States)

    Chen, Zhao; Xie, Zhipeng; Zhang, Jian

    2018-05-01

    The Vehicle-Bridge-Interaction (VBI) force, i.e., the normal contact force of a tire, is a key component in the VBI mechanism. The VBI force measurement can facilitate experimental studies of the VBI as well as input-output bridge structural identification. This paper introduces an innovative method for calculating the interaction force by using dynamic tire pressure monitoring. The core idea of the proposed method combines the ideal gas law and a basic force model to build a relationship between the tire pressure and the VBI force. Then, unknown model parameters are identified by the Extended Kalman Filter using calibration data. A signal filter based on the wavelet analysis is applied to preprocess the effect that the tire rotation has on the pressure data. Two laboratory tests were conducted to check the proposed method's validity. The effects of different road irregularities, loads and forward velocities were studied. Under the current experiment setting, the proposed method was robust to different road irregularities, and the increase in load and velocity benefited the performance of the proposed method. A high-speed test further supported the use of this method in rapid bridge tests. Limitations of the derived theories and experiment were also discussed.

  11. A discrete force allocation algorithm for modelling wind turbines in computational fluid dynamics

    DEFF Research Database (Denmark)

    Réthoré, Pierre-Elouan; Sørensen, Niels N.

    2012-01-01

    at the position of the wind turbine rotor to estimate correctly the power production and the rotor loading. The method proposed in this paper solves this issue by spreading the force on the direct neighbouring cells and applying an equivalent pressure jump at the cell faces. This can potentially open......This paper describes an algorithm for allocating discrete forces in computational fluid dynamics (CFD). Discrete forces are useful in wind energy CFD. They are used as an approximation of the wind turbine blades’ action on the wind (actuator disc/line), to model forests and to model turbulent...

  12. Cellular adhesome screen identifies critical modulators of focal adhesion dynamics, cellular traction forces and cell migration behaviour

    Science.gov (United States)

    Fokkelman, Michiel; Balcıoğlu, Hayri E.; Klip, Janna E.; Yan, Kuan; Verbeek, Fons J.; Danen, Erik H. J.; van de Water, Bob

    2016-01-01

    Cancer cells migrate from the primary tumour into surrounding tissue in order to form metastasis. Cell migration is a highly complex process, which requires continuous remodelling and re-organization of the cytoskeleton and cell-matrix adhesions. Here, we aimed to identify genes controlling aspects of tumour cell migration, including the dynamic organization of cell-matrix adhesions and cellular traction forces. In a siRNA screen targeting most cell adhesion-related genes we identified 200+ genes that regulate size and/or dynamics of cell-matrix adhesions in MCF7 breast cancer cells. In a subsequent secondary screen, the 64 most effective genes were evaluated for growth factor-induced cell migration and validated by tertiary RNAi pool deconvolution experiments. Four validated hits showed significantly enlarged adhesions accompanied by reduced cell migration upon siRNA-mediated knockdown. Furthermore, loss of PPP1R12B, HIPK3 or RAC2 caused cells to exert higher traction forces, as determined by traction force microscopy with elastomeric micropillar post arrays, and led to considerably reduced force turnover. Altogether, we identified genes that co-regulate cell-matrix adhesion dynamics and traction force turnover, thereby modulating overall motility behaviour. PMID:27531518

  13. Integrin and glycocalyx mediated contributions to cell adhesion identified by single cell force spectroscopy

    International Nuclear Information System (INIS)

    Boettiger, D; Wehrle-Haller, B

    2010-01-01

    The measurement of cell adhesion using single cell force spectroscopy methods was compared with earlier methods for measuring cell adhesion. This comparison provided a means and rationale for separating components of the measurement retract curve that were due to interactions between the substrate and the glycocalyx, and interactions that were due to cell surface integrins binding to a substrate-bound ligand. The glycocalyx adhesion was characterized by multiple jumps with dispersed jump sizes that extended from 5 to 30 μm from the origin. The integrin mediated adhesion was represented by the F max (maximum detachment force), was generally within the first 5 μm and commonly detached with a single rupture cascade. The integrin peak (F max ) increases with time and the rate of increase shows large cell to cell variability with a peak ∼ 50 nN s -1 and an average rate of increase of 75 pN s -1 . This is a measure of the rate of increase in the number of adhesive integrin-ligand bonds/cell as a function of contact time.

  14. Influence of surfactants in forced dynamic dewetting.

    Science.gov (United States)

    Henrich, Franziska; Fell, Daniela; Truszkowska, Dorota; Weirich, Marcel; Anyfantakis, Manos; Nguyen, Thi-Huong; Wagner, Manfred; Auernhammer, Günter K; Butt, Hans-Jürgen

    2016-09-20

    In this work we show that the forced dynamic dewetting of surfactant solutions depends sensitively on the surfactant concentration. To measure this effect, a hydrophobic rotating cylinder was horizontally half immersed in aqueous surfactant solutions. Dynamic contact angles were measured optically by extrapolating the contour of the meniscus to the contact line. Anionic (sodium 1-decanesulfonate, S-1DeS), cationic (cetyl trimethylammonium bromide, CTAB) and nonionic surfactants (C 4 E 1 , C 8 E 3 and C 12 E 5 ) with critical micelle concentrations (CMCs) spanning four orders of magnitude were used. The receding contact angle in water decreased with increasing velocity. This decrease was strongly enhanced when adding surfactant, even at surfactant concentrations of 10% of the critical micelle concentration. Plots of the receding contact angle-versus-velocity almost superimpose when being plotted at the same relative concentration (concentration/CMC). Thus the rescaled concentration is the dominating property for dynamic dewetting. The charge of the surfactants did not play a role, thus excluding electrostatic effects. The change in contact angle can be interpreted by local surface tension gradients, i.e. Marangoni stresses, close to the three-phase contact line. The decrease of dynamic contact angles with velocity follows two regimes. Despite the existence of Marangoni stresses close to the contact line, for a dewetting velocity above 1-10 mm s -1 the hydrodynamic theory is able to describe the experimental results for all surfactant concentrations. At slower velocities an additional steep decrease of the contact angle with velocity was observed. Particle tracking velocimetry showed that the flow profiles do not differ with and without surfactant on a scales >100 μm.

  15. Interacting trophic forcing and the population dynamics of herring

    DEFF Research Database (Denmark)

    Lindegren, Martin; Ostman, Orjan; Gardmark, Anna

    2011-01-01

    -up nor top-down, but rather through multiple external and internal drivers. While in many studies single drivers have been identified, potential synergies of multiple factors, as well as their relative importance in regulating population dynamics of small pelagic fish, is a largely unresolved issue....... Using a statistical, age-structured modeling approach, we demonstrate the relative importance and influence of bottom-up (e.g., climate, zooplankton availability) and top-down (i.e., fishing and predation) factors on the population dynamics of Bothnian Sea herring (Clupea harengus) throughout its life...... cycle. Our results indicate significant bottom-up effects of zooplankton and interspecific competition from sprat (Sprattus sprattus), particularly on younger age classes of herring. Although top-down forcing through fishing and predation by grey seals (Halichoerus grypus) and Atlantic cod (Gadus morhua...

  16. Ultrafast carrier dynamics of titanic acid nanotubes investigated by transient absorption spectroscopy.

    Science.gov (United States)

    Wang, Li; Zhao, Hui; Pan, Lin Yun; Weng, Yu Xiang; Nakato, Yoshihiro; Tamai, Naoto

    2010-12-01

    Carrier dynamics of titanic acid nanotubes (phase of H2Ti2O5.H2O) deposited on a quartz plate was examined by visible/near-IR transient absorption spectroscopy with an ultraviolet excitation. The carrier dynamics of titanic acid nanotubes follows the fast trapping process which attributed to the intrinsic tubular structure, the relaxation of shallow trapped carriers and the recombination as a second-order kinetic process. Transient absorption of titanic acid nanotubes was dominated by the absorption of surface-trapped holes in visible region around 500 nm, which was proved by the faster decay dynamics in the presence of polyvinyl alcohol as a hole-scavenger. However, the slow relaxation of free carriers was much more pronounced in the TiO2 single crystals, as compared with the transient absorption spectra of titanic acid nanotubes under the similar excitation.

  17. Characterization of the ground state dynamics of proteorhodopsin by NMR and optical spectroscopies

    International Nuclear Information System (INIS)

    Stehle, Jochen; Scholz, Frank; Löhr, Frank; Reckel, Sina; Roos, Christian; Blum, Michaela; Braun, Markus; Glaubitz, Clemens; Dötsch, Volker; Wachtveitl, Josef; Schwalbe, Harald

    2012-01-01

    We characterized the dynamics of proteorhodopsin (PR), solubilized in diC7PC, a detergent micelle, by liquid-state NMR spectroscopy at T = 323 K. Insights into the dynamics of PR at different time scales could be obtained and dynamic hot spots could be identified at distinct, functionally relevant regions of the protein, including the BC loop, the EF loop, the N-terminal part of helix F and the C-terminal part of helix G. We further characterize the dependence of the photocycle on different detergents (n-Dodecyl β-D-maltoside DDM; 1,2-diheptanoyl-sn-glycero-3-phosphocholine diC7PC) by ultrafast time-resolved UV/VIS spectroscopy. While the photocycle intermediates of PR in diC7PC and DDM exhibit highly similar spectral characteristics, significant changes in the population of these intermediates are observed. In-situ NMR experiments have been applied to characterize structural changes during the photocycle. Light-induced chemical shift changes detected during the photocycle in diC7PC are very small, in line with the changes in the population of intermediates in the photocycle of proteorhodopsin in diC7PC, where the late O-intermediate populated in DDM is missing and the population is shifted towards an equilibrium of intermediates states (M, N, O) without accumulation of a single populated intermediate.

  18. A device for testing the dynamic performance of in situ force plates.

    Science.gov (United States)

    East, Rebecca H; Noble, Jonathan J; Arscott, Richard A; Shortland, Adam P

    2017-09-01

    Force plates are often incorporated into motion capture systems for the calculation of joint kinetic variables and other data. This project aimed to create a system that could be used to check the dynamic performance of force plate in situ. The proposed solution involved the design and development of an eccentrically loaded wheel mounted on a weighted frame. The frame was designed to hold a wheel mounted in two orthogonal positions. The wheel was placed on the force plate and spun. A VICON™ motion analysis system captured the positional data of the markers placed around the rim of the wheel which was used to create a simulated force profile, and the force profile was dependent on spin speed. The root mean square error between the simulated force profile and the force plate measurement was calculated. For nine trials conducted, the root mean square error between the two simultaneous measures of force was calculated. The difference between the force profiles in the x- and y-directions is approximately 2%. The difference in the z-direction was under 0.5%. The eccentrically loaded wheel produced a predictable centripetal force in the plane of the wheel which varied in direction as the wheel was spun and magnitude dependent on the spin speed. There are three important advantages to the eccentrically loaded wheel: (1) it does not rely on force measurements made from other devices, (2) the tests require only 15 min to complete per force plate and (3) the forces exerted on the plate are similar to those of paediatric gait.

  19. Fourier Transform Infrared (FTIR) Spectroscopy, Ultraviolet Resonance Raman (UVRR) Spectroscopy, and Atomic Force Microscopy (AFM) for Study of the Kinetics of Formation and Structural Characterization of Tau Fibrils.

    Science.gov (United States)

    Ramachandran, Gayathri

    2017-01-01

    Kinetic studies of tau fibril formation in vitro most commonly employ spectroscopic probes such as thioflavinT fluorescence and laser light scattering or negative stain transmission electron microscopy. Here, I describe the use of Fourier transform infrared (FTIR) spectroscopy, ultraviolet resonance Raman (UVRR) spectroscopy, and atomic force microscopy (AFM) as complementary probes for studies of tau aggregation. The sensitivity of vibrational spectroscopic techniques (FTIR and UVRR) to secondary structure content allows for measurement of conformational changes that occur when the intrinsically disordered protein tau transforms into cross-β-core containing fibrils. AFM imaging serves as a gentle probe of structures populated over the time course of tau fibrillization. Together, these assays help further elucidate the structural and mechanistic complexity inherent in tau fibril formation.

  20. Chromatin dynamics resolved with force spectroscopy

    NARCIS (Netherlands)

    Chien, Fan-Tso

    2011-01-01

    In eukaryotic cells, genomic DNA is organized in chromatin fibers composed of nucleosomes as structural units. A nucleosome contains 1.7 turns of DNA wrapped around a histone octamer and is connected to the adjacent nucleosomes with linker DNA. The folding of chromatin fibers effectively increases

  1. Identification of the nonlinear excitation force acting on a bowed string using the dynamical responses at remote locations

    International Nuclear Information System (INIS)

    Debut, V.; Antunes, J.; Delaune, X.

    2010-01-01

    For achieving realistic numerical simulations of bowed string instruments, based on physical modeling, a good understanding of the actual friction interaction phenomena is of great importance. Most work published in the field including our own has assumed that bow/string frictional forces behave according to the classical Coulomb stick-slip model, with an empirical velocity-dependent sliding friction coefficient. Indeed, the basic self-excited string motions (such as the Helmholtz regime) are well captured using such friction model. However, recent work has shown that the tribological behavior of the bow/string rosin interface is rather complex, therefore the basic velocity-dependent Coulomb model may be an over-simplistic representation of the friction force. More specifically, it was suggested that a more accurate model of the interaction force can be achieved by coupling the system dynamical equations with a thermal model which encapsulates the complex interface phenomena. In spite of the interesting work performed by Askenfelt, a direct measurement of the actual dynamical friction forces without disturbing the string motion is quite difficult. Therefore, in this work we develop a modal-based identification technique making use of inverse methods and optimization techniques, which enables the identification of the interface force, as well as the string self-excited motion, from the dynamical reactions measured at the string end supports. The method gives convincing results using simulated data originated from nonlinear computations of a bowed string. Furthermore, in cases where the force identifications are very sensitive to errors in the transfer function modal parameters, we suggest a method to improve the modal frequencies used for the identifications. Preliminary experimental results obtained using a basic bowing device, by which the string is excited with the stick of the bow, are then presented. Our identifications, from the two dynamical string reactions

  2. Nonlinear Dynamical Analysis for the Cable Excited with Parametric and Forced Excitation

    Directory of Open Access Journals (Sweden)

    C. Z. Qian

    2014-01-01

    Full Text Available Considering the deck vibration effect on the cable in cable-stayed bridge, using nonlinear structure dynamics theory, the nonlinear dynamical equation for the stayed cable excited with deck vibration is proposed. Research shows that the vertical vibration of the deck has a combined parametric and forced excitation effect on the cable when the angle of the cable is taken into consideration. Using multiscale method, the 1/2 principle parametric resonance is studied and the bifurcation equation is obtained. Despite the parameters analysis, the bifurcation characters of the dynamical system are studied. At last, by means of numerical method and software MATHMATIC, the effect rules of system parameters to the dynamical behavior of the system are studied, and some useful conclusions are obtained.

  3. A dynamic force balance model for colloidal expansion and its DLVO-based application.

    Science.gov (United States)

    Liu, Longcheng; Moreno, Luis; Neretnieks, Ivars

    2009-01-20

    A force balance model that describes the dynamic expansion of colloidal bentonite gels/sols is presented. The colloidal particles are assumed to consist of one or several thin sheets with the other dimensions much larger than their thickness. The forces considered include van der Waals force, diffuse double layer force, thermal force giving rise to Brownian motion, gravity, as well as friction force. The model results in an expression resembling the instationary diffusion equation but with an immensely variable diffusivity. This diffusivity is strongly influenced by the concentration of counterions as well as by the particle concentration in the colloid gel/sol. The properties of the model are explored and discussed, exemplified by the upward expansion of an originally highly compacted bentonite tablet in a test tube. Examples are presented for a number of cases with ionic concentrations varying between very dilute waters up to several molar of counterions. The volume fraction of particles ranges from 40% to very dilute sols.

  4. Selecting a Dynamic Simulation Modeling Method for Health Care Delivery Research—Part 2: Report of the ISPOR Dynamic Simulation Modeling Emerging Good Practices Task Force

    NARCIS (Netherlands)

    Marshall, Deborah A.; Burgos-Liz, Lina; IJzerman, Maarten Joost; Crown, William; Padula, William V.; Wong, Peter K.; Pasupathy, Kalyan S.; Higashi, Mitchell K.; Osgood, Nathaniel D.

    2015-01-01

    In a previous report, the ISPOR Task Force on Dynamic Simulation Modeling Applications in Health Care Delivery Research Emerging Good Practices introduced the fundamentals of dynamic simulation modeling and identified the types of health care delivery problems for which dynamic simulation modeling

  5. Kelvin probe force microscopy in liquid using electrochemical force microscopy

    Directory of Open Access Journals (Sweden)

    Liam Collins

    2015-01-01

    Full Text Available Conventional closed loop-Kelvin probe force microscopy (KPFM has emerged as a powerful technique for probing electric and transport phenomena at the solid–gas interface. The extension of KPFM capabilities to probe electrostatic and electrochemical phenomena at the solid–liquid interface is of interest for a broad range of applications from energy storage to biological systems. However, the operation of KPFM implicitly relies on the presence of a linear lossless dielectric in the probe–sample gap, a condition which is violated for ionically-active liquids (e.g., when diffuse charge dynamics are present. Here, electrostatic and electrochemical measurements are demonstrated in ionically-active (polar isopropanol, milli-Q water and aqueous NaCl and ionically-inactive (non-polar decane liquids by electrochemical force microscopy (EcFM, a multidimensional (i.e., bias- and time-resolved spectroscopy method. In the absence of mobile charges (ambient and non-polar liquids, KPFM and EcFM are both feasible, yielding comparable contact potential difference (CPD values. In ionically-active liquids, KPFM is not possible and EcFM can be used to measure the dynamic CPD and a rich spectrum of information pertaining to charge screening, ion diffusion, and electrochemical processes (e.g., Faradaic reactions. EcFM measurements conducted in isopropanol and milli-Q water over Au and highly ordered pyrolytic graphite electrodes demonstrate both sample- and solvent-dependent features. Finally, the feasibility of using EcFM as a local force-based mapping technique of material-dependent electrostatic and electrochemical response is investigated. The resultant high dimensional dataset is visualized using a purely statistical approach that does not require a priori physical models, allowing for qualitative mapping of electrostatic and electrochemical material properties at the solid–liquid interface.

  6. Identification of Object Dynamics Using Hand Worn Motion and Force Sensors

    Directory of Open Access Journals (Sweden)

    Henk G. Kortier

    2016-11-01

    Full Text Available Emerging microelectromechanical system (MEMS-based sensors become much more applicable for on-body measurement purposes lately. Especially, the development of a finger tip-sized tri-axial force sensor gives the opportunity to measure interaction forces between the human hand and environmental objects. We have developed a new prototype device that allows simultaneous 3D force and movement measurements at the finger and thumb tips. The combination of interaction forces and movements makes it possible to identify the dynamical characteristics of the object being handled by the hand. With this device attached to the hand, a subject manipulated mass and spring objects under varying conditions. We were able to identify and estimate the weight of two physical mass objects (0.44 kg: 29 . 3 % ± 18 . 9 % and 0.28 kg: 19 . 7 % ± 10 . 6 % and the spring constant of a physical spring object ( 16 . 3 % ± 12 . 6 % . The system is a first attempt to quantify the interactions of the hand with the environment and has many potential applications in rehabilitation, ergonomics and sports.

  7. How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?

    NARCIS (Netherlands)

    Villa, Alessandra; Fan, Hao; Wassenaar, Tsjerk; Mark, Alan E.

    2007-01-01

    The sensitivity of molecular dynamics simulations to variations in the force field has been examined in relation to a set of 36 structures corresponding to 31 proteins simulated by using different versions of the GROMOS force field. The three parameter sets used (43a1, 53a5, and 53a6) differ

  8. A phenomenological approach to modeling chemical dynamics in nonlinear and two-dimensional spectroscopy.

    Science.gov (United States)

    Ramasesha, Krupa; De Marco, Luigi; Horning, Andrew D; Mandal, Aritra; Tokmakoff, Andrei

    2012-04-07

    We present an approach for calculating nonlinear spectroscopic observables, which overcomes the approximations inherent to current phenomenological models without requiring the computational cost of performing molecular dynamics simulations. The trajectory mapping method uses the semi-classical approximation to linear and nonlinear response functions, and calculates spectra from trajectories of the system's transition frequencies and transition dipole moments. It rests on identifying dynamical variables important to the problem, treating the dynamics of these variables stochastically, and then generating correlated trajectories of spectroscopic quantities by mapping from the dynamical variables. This approach allows one to describe non-Gaussian dynamics, correlated dynamics between variables of the system, and nonlinear relationships between spectroscopic variables of the system and the bath such as non-Condon effects. We illustrate the approach by applying it to three examples that are often not adequately treated by existing analytical models--the non-Condon effect in the nonlinear infrared spectra of water, non-Gaussian dynamics inherent to strongly hydrogen bonded systems, and chemical exchange processes in barrier crossing reactions. The methods described are generally applicable to nonlinear spectroscopy throughout the optical, infrared and terahertz regions.

  9. Control of phase transition dynamics in media with nanoscale nonuniformities by coherence loss spectroscopy

    International Nuclear Information System (INIS)

    Brodsky, Anatol M

    2010-01-01

    The optical nondestructive characterization of chemical transformation dynamics and diffusion kinetics, including phase transitions, in heterogeneous media with a random distribution of nanoparticles (nano-nonuniformities), is of great theoretical and practical importance. Such characterization, with the help of coherence loss spectroscopy, considered in this paper can be applied for the control of a number of industrial processes dynamics, environmental monitoring, and medical diagnostics and therapy. As a specific example, the growth of crystal nuclei (embrions) as a result of the diffusion to them of a substance from the surrounding supersaturated solution is considered

  10. On the Effectiveness of the Dynamic Force Adjustment for Reducing the Scatter of Instrumented Charpy Results

    International Nuclear Information System (INIS)

    Lucon, E.

    2008-01-01

    One of the key factors for obtaining reliable instrumented Charpy results is the calibration of the instrumented striker. An interesting alternative to the conventional static calibration recommended by the standards is the Dynamic Force Adjustment (DFA), in which forces and displacements are iteratively adjusted until equality is achieved between absorbed energies calculated under the test record (Wt) and measured by the machine encoder (KV). In this study, this procedure has been applied to the instrumented data obtained by 10 international laboratories using notched and precracked Charpy specimens, in the framework of a Coordinated Research Project (CRP8) of IAEA. DFA is extremely effective in reducing the between-laboratory scatter for both general yield and maximum forces. The effect is less significant for dynamic reference temperatures measured from precracked Charpy specimens using the Master Curve procedure, but a moderate reduction of the standard deviation is anyway observed. It is shown that striker calibration is a prominent contribution to the interlaboratory variability of instrumented impact forces, particularly in the case of maximum forces.

  11. On the Effectiveness of the Dynamic Force Adjustment for Reducing the Scatter of Instrumented Charpy Results

    Energy Technology Data Exchange (ETDEWEB)

    Lucon, E.

    2008-09-15

    One of the key factors for obtaining reliable instrumented Charpy results is the calibration of the instrumented striker. An interesting alternative to the conventional static calibration recommended by the standards is the Dynamic Force Adjustment (DFA), in which forces and displacements are iteratively adjusted until equality is achieved between absorbed energies calculated under the test record (Wt) and measured by the machine encoder (KV). In this study, this procedure has been applied to the instrumented data obtained by 10 international laboratories using notched and precracked Charpy specimens, in the framework of a Coordinated Research Project (CRP8) of IAEA. DFA is extremely effective in reducing the between-laboratory scatter for both general yield and maximum forces. The effect is less significant for dynamic reference temperatures measured from precracked Charpy specimens using the Master Curve procedure, but a moderate reduction of the standard deviation is anyway observed. It is shown that striker calibration is a prominent contribution to the interlaboratory variability of instrumented impact forces, particularly in the case of maximum forces.

  12. Fluorescence Spectroscopy, Exciton Dynamics and Photochemistry of Single Allophycocyanin Trimers

    International Nuclear Information System (INIS)

    Ying, Liming; Xie, Xiaoliang

    1998-01-01

    We report a study of the spectroscopy and exciton dynamics of the allophycocyanin trimer (APC), a light harvesting protein complex from cyanobacteria, by room-temperature single-molecule measurements of fluorescence spectra, lifetimes, intensity trajectories and polarization modulation. Emission spectra of individual APC trimers are found to be homogeneous on the time scale of seconds. In contrast, their emission lifetimes are found to be widely distributed, because of generation of exciton traps during the course of measurements. The intensity trajectories and polarization modulation experiments indicate reversible ixciton trap formation within the three quasi-independent pairs of strong interacting a84 and B84 chromophores in APC, as well a photobleaching of individual chromophores. Comparison experiments under continuous wave and pulsed excitation reveal a two-photon mechanism for generating exciton traps and/or photobleaching, which involves exciton-exciton annihilation. These single-molecule experiments provide new insights into exciton dynamics and photochemistry of light-harvesting complexes

  13. Pump–probe microscopy: Visualization and spectroscopy of ultrafast dynamics at the nanoscale

    Energy Technology Data Exchange (ETDEWEB)

    Grumstrup, Erik M., E-mail: erik.grumstrup@montana.edu [Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59718 (United States); Gabriel, Michelle M.; Cating, Emma E.M.; Van Goethem, Erika M. [Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 (United States); Papanikolas, John M., E-mail: john_papanikolas@unc.edu [Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 (United States)

    2015-09-08

    Highlights: • Diffraction limited pump–probe microscopy methods are described. • Spatial variation in dynamical phenomena across single structures. • Direct observation of carrier motion in individual nanostructures. - Abstract: Excited state dynamics at the nanoscale provide important insight into the influence of structural features such as interfaces, defects, and surfaces on material properties. Pump–probe microscopy combines the spatial resolution of far-field optical microscopy with the temporal resolution of ultrafast spectroscopy, and has emerged as a powerful technique for characterizing spatial variation in dynamical phenomena across nanometer length scales. It has helped correlate dynamical phenomena with specific structural features in a variety of materials, shedding light on how excited state behaviors can dramatically differ from one member of the ensemble to the next, and even at different points within a single structure. It has also enabled direct imaging of transport phenomena such as free carrier diffusion, exciton migration and plasmon propagation in nanostructures. This ability to observe individual objects provides unique insight into complex materials where heterogeneous behavior makes it difficult, if not impossible, to reach clear and quantitative conclusions.

  14. Vibrational dynamics of aqueous hydroxide solutions probed using broadband 2DIR spectroscopy

    International Nuclear Information System (INIS)

    Mandal, Aritra; Tokmakoff, Andrei

    2015-01-01

    We employed ultrafast transient absorption and broadband 2DIR spectroscopy to study the vibrational dynamics of aqueous hydroxide solutions by exciting the O–H stretch vibrations of the strongly hydrogen-bonded hydroxide solvation shell water and probing the continuum absorption of the solvated ion between 1500 and 3800 cm −1 . We observe rapid vibrational relaxation processes on 150–250 fs time scales across the entire probed spectral region as well as slower vibrational dynamics on 1–2 ps time scales. Furthermore, the O–H stretch excitation loses its frequency memory in 180 fs, and vibrational energy exchange between bulk-like water vibrations and hydroxide-associated water vibrations occurs in ∼200 fs. The fast dynamics in this system originate in strong nonlinear coupling between intra- and intermolecular vibrations and are explained in terms of non-adiabatic vibrational relaxation. These measurements indicate that the vibrational dynamics of the aqueous hydroxide complex are faster than the time scales reported for long-range transport of protons in aqueous hydroxide solutions

  15. Static and Dynamic Measurement of Dopamine Adsorption in Carbon Fiber Microelectrodes Using Electrochemical Impedance Spectroscopy.

    Science.gov (United States)

    Rivera-Serrano, Nilka; Pagan, Miraida; Colón-Rodríguez, Joanisse; Fuster, Christian; Vélez, Román; Almodovar-Faria, Jose; Jiménez-Rivera, Carlos; Cunci, Lisandro

    2018-02-06

    In this study, electrochemical impedance spectroscopy was used for the first time to study the adsorption of dopamine in carbon fiber microelectrodes. In order to show a proof-of-concept, static and dynamic measurements were taken at potentials ranging from -0.4 to 0.8 V versus Ag|AgCl to demonstrate the versatility of this technique to study dopamine without the need of its oxidation. We used electrochemical impedance spectroscopy and single frequency electrochemical impedance to measure different concentrations of dopamine as low as 1 nM. Moreover, the capacitance of the microelectrodes surface was found to decrease due to dopamine adsorption, which is dependent on its concentration. The effect of dissolved oxygen and electrochemical oxidation of the surface in the detection of dopamine was also studied. Nonoxidized and oxidized carbon fiber microelectrodes were prepared and characterized by optical microscopy, scanning electron microscopy, cyclic voltammetry, and electrochemical impedance spectroscopy. Optimum working parameters of the electrodes, such as frequency and voltage, were obtained for better measurement. Electrochemical impedance of dopamine was determined at different concentration, voltages, and frequencies. Finally, dynamic experiments were conducted using a flow cell and single frequency impedance in order to study continuous and real-time measurements of dopamine.

  16. Slow Aging Dynamics and Avalanches in a Gold-Cadmium Alloy Investigated by X-Ray Photon Correlation Spectroscopy

    International Nuclear Information System (INIS)

    Mueller, L.; Waldorf, M.; Klemradt, U.; Gutt, C.; Gruebel, G.; Madsen, A.; Finlayson, T. R.

    2011-01-01

    Results of a x-ray photon correlation spectroscopy experiment on the very weakly first order martensitic transformation of a Au 50.5 Cd 49.5 single crystal are presented. Slow non-equilibrium-dynamics are observed in a narrow temperature interval in the direct vicinity of the otherwise athermal phase transformation. These dynamics are associated with the martensite-aging effect. The dynamical aging is accompanied by an avalanchelike behavior which is identified with an incubation-time phenomenon.

  17. Slow aging dynamics and avalanches in a gold-cadmium alloy investigated by x-ray photon correlation spectroscopy.

    Science.gov (United States)

    Müller, L; Waldorf, M; Gutt, C; Grübel, G; Madsen, A; Finlayson, T R; Klemradt, U

    2011-09-02

    Results of a x-ray photon correlation spectroscopy experiment on the very weakly first order martensitic transformation of a Au50.5Cd49.5 single crystal are presented. Slow non-equilibrium-dynamics are observed in a narrow temperature interval in the direct vicinity of the otherwise athermal phase transformation. These dynamics are associated with the martensite-aging effect. The dynamical aging is accompanied by an avalanchelike behavior which is identified with an incubation-time phenomenon.

  18. On the dynamic fracture toughness and crack tip strain behavior of nuclear pressure vessel steel: Application of electromagnetic force

    International Nuclear Information System (INIS)

    Yagawa, G.; Yoshimura, S.

    1986-01-01

    This paper is concerned with the application of the electromagnetic force to the determination of the dynamic fracture toughness of materials. Taken is an edge-cracked specimen which carries a transient electric current and is simply supported in a steady magnetic field. As a result of their interaction, the dynamic electromagnetic force occurs in the whole body of the specimen, which is then deformed to fracture in the opening mode of cracking. Using the electric potential and the J-R curve methods to determine the dynamic crack initiation point in the experiment, together with the finite element method to calculate the extended J-integral with the effects of the electromagnetic force and inertia, the dynamic fracture toughness values of nuclear pressure vessel steel A508 class 3 are evaluated over a wide temperature range from lower to upper shelves. The strain distribution near the crack tip in the dynamic process of fracture is also obtained by applying a computer picture processing. (orig.)

  19. Lattice dynamic studies from {sup 151}Eu-Moessbauer spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Katada, Motomi [Tokyo Metropolitan Univ., Hachioji (Japan). Faculty of Science

    1997-03-01

    New complexes {l_brace}(Eu(napy){sub 2}(H{sub 2}O){sub 3})(Fe(CN){sub 6})4H{sub 2}O{r_brace}{sub x}, bpy({l_brace}(Eu(bpy)(H{sub 2}O){sub 4})(Fe(CN){sub 6})1.5bpy4H{sub 2}O{r_brace}{sub x}) and ({l_brace}(Eu(phen){sub 2}(H{sub 2}O){sub 2})(Fe(CN){sub 6})2phen{r_brace}{sub x}) etc were synthesized using phenanthroline and bipyridine. Lattice dynamic behaviors of Eu and Fe atom in the complexes were investigated by Moessbauer spectroscopy. By {sup 151}Eu-Moessbauer spectrum and parameters of new complexes, bpy complex showed the largest quadrupole splitting value, indicating bad symmetry of Eu ligand in the environment. Molecular structure of napy, bpy and phen complex were shown. These complexes are consisted of Eu atom coordinated with ligand and water molecule, of which (Fe(CN){sub 6}){sup 3-} ion formed one dimentional polymer chain and naphthyridines formed stacking structure. New complexes were observed by {sup 57}Fe-Moessbauer spectroscopy, too. The quadrupole splitting values were very different each other, indicating change of symmetry of Fe atom in the environment and three valence low spin state of Fe in the complex. (S.Y.)

  20. 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.

  1. 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

  2. Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.

    Science.gov (United States)

    Kukic, Predrag; Kannan, Arvind; Dijkstra, Maurits J J; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

    2015-10-01

    It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost.

  3. Force-Induced Unravelling of DNA Origami.

    Science.gov (United States)

    Engel, Megan C; Smith, David M; Jobst, Markus A; Sajfutdinow, Martin; Liedl, Tim; Romano, Flavio; Rovigatti, Lorenzo; Louis, Ard A; Doye, Jonathan P K

    2018-05-31

    The mechanical properties of DNA nanostructures are of widespread interest as applications that exploit their stability under constant or intermittent external forces become increasingly common. We explore the force response of DNA origami in comprehensive detail by combining AFM single molecule force spectroscopy experiments with simulations using oxDNA, a coarse-grained model of DNA at the nucleotide level, to study the unravelling of an iconic origami system: the Rothemund tile. We contrast the force-induced melting of the tile with simulations of an origami 10-helix bundle. Finally, we simulate a recently-proposed origami biosensor, whose function takes advantage of origami behaviour under tension. We observe characteristic stick-slip unfolding dynamics in our force-extension curves for both the Rothemund tile and the helix bundle and reasonable agreement with experimentally observed rupture forces for these systems. Our results highlight the effect of design on force response: we observe regular, modular unfolding for the Rothemund tile that contrasts with strain-softening of the 10-helix bundle which leads to catastropic failure under monotonically increasing force. Further, unravelling occurs straightforwardly from the scaffold ends inwards for the Rothemund tile, while the helix bundle unfolds more nonlinearly. The detailed visualization of the yielding events provided by simulation allows preferred pathways through the complex unfolding free-energy landscape to be mapped, as a key factor in determining relative barrier heights is the extensional release per base pair broken. We shed light on two important questions: how stable DNA nanostructures are under external forces; and what design principles can be applied to enhance stability.

  4. Vehicle Sliding Mode Control with Adaptive Upper Bounds: Static versus Dynamic Allocation to Saturated Tire Forces

    Directory of Open Access Journals (Sweden)

    Ali Tavasoli

    2012-01-01

    Full Text Available Nonlinear vehicle control allocation is achieved through distributing the task of vehicle control among individual tire forces, which are constrained to nonlinear saturation conditions. A high-level sliding mode control with adaptive upper bounds is considered to assess the body yaw moment and lateral force for the vehicle motion. The proposed controller only requires the online adaptation of control gains without acquiring the knowledge of upper bounds on system uncertainties. Static and dynamic control allocation approaches have been formulated to distribute high-level control objectives among the system inputs. For static control allocation, the interior-point method is applied to solve the formulated nonlinear optimization problem. Based on the dynamic control allocation method, a dynamic update law is derived to allocate vehicle control to tire forces. The allocated tire forces are fed into a low-level control module, where the applied torque and active steering angle at each wheel are determined through a slip-ratio controller and an inverse tire model. Computer simulations are used to prove the significant effects of the proposed control allocation methods on improving the stability and handling performance. The advantages and limitations of each method have been discussed, and conclusions have been derived.

  5. Decomposition principles applied to the dynamic production and work-force scheduling problem

    NARCIS (Netherlands)

    Aardal, K.I.; Ari, A.

    1987-01-01

    One of the most important problems in the production and inventory planning field, is the scheduling of production and work force in a dynamic environment. Although this problem can be formulated as a linear program, it is often quite difficult to solve directly, due to its large scale. Instead, it

  6. Effect of three-body forces on the lattice dynamics of noble metals

    Indian Academy of Sciences (India)

    A simple method to generate an effective electron–ion interaction pseudopotential from the energy wave number characteristic obtained by first principles calculations has been suggested. This effective potential has been used, in third order perturbation, to study the effect of three-body forces on the lattice dynamics of ...

  7. Preventing disulfide bond formation weakens non-covalent forces among lysozyme aggregates.

    Directory of Open Access Journals (Sweden)

    Vijay Kumar Ravi

    Full Text Available Nonnative disulfide bonds have been observed among protein aggregates in several diseases like amyotrophic lateral sclerosis, cataract and so on. The molecular mechanism by which formation of such bonds promotes protein aggregation is poorly understood. Here in this work we employ previously well characterized aggregation of hen eggwhite lysozyme (HEWL at alkaline pH to dissect the molecular role of nonnative disulfide bonds on growth of HEWL aggregates. We employed time-resolved fluorescence anisotropy, atomic force microscopy and single-molecule force spectroscopy to quantify the size, morphology and non-covalent interaction forces among the aggregates, respectively. These measurements were performed under conditions when disulfide bond formation was allowed (control and alternatively when it was prevented by alkylation of free thiols using iodoacetamide. Blocking disulfide bond formation affected growth but not growth kinetics of aggregates which were ∼50% reduced in volume, flatter in vertical dimension and non-fibrillar in comparison to control. Interestingly, single-molecule force spectroscopy data revealed that preventing disulfide bond formation weakened the non-covalent interaction forces among monomers in the aggregate by at least ten fold, thereby stalling their growth and yielding smaller aggregates in comparison to control. We conclude that while constrained protein chain dynamics in correctly disulfide bonded amyloidogenic proteins may protect them from venturing into partial folded conformations that can trigger entry into aggregation pathways, aberrant disulfide bonds in non-amyloidogenic proteins (like HEWL on the other hand, may strengthen non-covalent intermolecular forces among monomers and promote their aggregation.

  8. AFM force spectroscopy reveals how subtle structural differences affect the interaction strength between Candida albicans and DC-SIGN.

    Science.gov (United States)

    te Riet, Joost; Reinieren-Beeren, Inge; Figdor, Carl G; Cambi, Alessandra

    2015-11-01

    The fungus Candida albicans is the most common cause of mycotic infections in immunocompromised hosts. Little is known about the initial interactions between Candida and immune cell receptors, such as the C-type lectin dendritic cell-specific intracellular cell adhesion molecule-3 (ICAM-3)-grabbing non-integrin (DC-SIGN), because a detailed characterization at the structural level is lacking. DC-SIGN recognizes specific Candida-associated molecular patterns, that is, mannan structures present in the cell wall of Candida. The molecular recognition mechanism is however poorly understood. We postulated that small differences in mannan-branching may result in considerable differences in the binding affinity. Here, we exploit atomic force microscope-based dynamic force spectroscopy with single Candida cells to gain better insight in the carbohydrate recognition capacity of DC-SIGN. We demonstrate that slight differences in the N-mannan structure of Candida, that is, the absence or presence of a phosphomannan side chain, results in differences in the recognition by DC-SIGN as follows: (i) it contributes to the compliance of the outer cell wall of Candida, and (ii) its presence results in a higher binding energy of 1.6 kB T. The single-bond affinity of tetrameric DC-SIGN for wild-type C. albicans is ~10.7 kB T and a dissociation constant kD of 23 μM, which is relatively strong compared with other carbohydrate-protein interactions described in the literature. In conclusion, this study shows that DC-SIGN specifically recognizes mannan patterns on C. albicans with high affinity. Knowledge on the binding pocket of DC-SIGN and its pathogenic ligands will lead to a better understanding of how fungal-associated carbohydrate structures are recognized by receptors of the immune system and can ultimately contribute to the development of new anti-fungal drugs. Copyright © 2015 John Wiley & Sons, Ltd.

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

    Science.gov (United States)

    Miri, MirFaez; Nekouie, Vahid; Golestanian, Ramin

    2010-01-01

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

  10. Probabilistic information on object weight shapes force dynamics in a grip-lift task.

    Science.gov (United States)

    Trampenau, Leif; Kuhtz-Buschbeck, Johann P; van Eimeren, Thilo

    2015-06-01

    Advance information, such as object weight, size and texture, modifies predictive scaling of grip forces in a grip-lift task. Here, we examined the influence of probabilistic advance information about object weight. Fifteen healthy volunteers repeatedly grasped and lifted an object equipped with a force transducer between their thumb and index finger. Three clearly distinguishable object weights were used. Prior to each lift, the probabilities for the three object weights were given by a visual cue. We examined the effect of probabilistic pre-cues on grip and lift force dynamics. We expected predictive scaling of grip force parameters to follow predicted values calculated according to probabilistic contingencies of the cues. We observed that probabilistic cues systematically influenced peak grip and load force rates, as an index of predictive motor scaling. However, the effects of probabilistic cues on force rates were nonlinear, and anticipatory adaptations of the motor output generally seemed to overestimate high probabilities and underestimate low probabilities. These findings support the suggestion that anticipatory adaptations and force scaling of the motor system can integrate probabilistic information. However, probabilistic information seems to influence motor programs in a nonlinear fashion.

  11. MDM2–MDM4 molecular interaction investigated by atomic force spectroscopy and surface plasmon resonance

    Directory of Open Access Journals (Sweden)

    Moscetti I

    2016-08-01

    Full Text Available Ilaria Moscetti,1 Emanuela Teveroni,2,3 Fabiola Moretti,3 Anna Rita Bizzarri,1 Salvatore Cannistraro1 1Biophysics and Nanoscience Centre, Department DEB, Università della Tuscia, Viterbo, Italy; 2Department of Endocrinology and Metabolism, Università Cattolica di Roma, Roma, Italy; 3Institute of Cell Biology and Neurobiology, Consiglio Nazionale delle Ricerche (CNR, Roma, Italy Abstract: Murine double minute 2 (MDM2 and 4 (MDM4 are known as the main negative regulators of p53, a tumor suppressor. They are able to form heterodimers that are much more effective in the downregulation of p53. Therefore, the MDM2–MDM4 complex could be a target for promising therapeutic restoration of p53 function. To this aim, a deeper understanding of the molecular mechanisms underlining the heterodimerization is needed. The kinetic and thermodynamic characterization of the MDM2–MDM4 complex was performed with two complementary approaches: atomic force spectroscopy and surface plasmon resonance. Both techniques revealed an equilibrium dissociation constant (KD in the micromolar range for the MDM2–MDM4 heterodimer, similar to related complexes involved in the p53 network. Furthermore, the MDM2–MDM4 complex is characterized by a relatively high free energy, through a single energy barrier, and by a lifetime in the order of tens of seconds. New insights into the MDM2–MDM4 interaction could be highly important for developing innovative anticancer drugs focused on p53 reactivation. Keywords: MDM2, MDM4, atomic force spectroscopy, surface plasmon resonance

  12. Complex dynamics in three-well duffing system with two external forcings

    International Nuclear Information System (INIS)

    Jing Zhujun; Huang Jicai; Deng Jin

    2007-01-01

    Three-well duffing system with two external forcing terms is investigated. The criterion of existence of chaos under the periodic perturbation is given by using Melnikov's method. By using second-order averaging method and Melnikov's method we proved the criterion of existence of chaos in averaged systems under quasi-periodic perturbation for ω 2 = nω 1 + εν, n = 1, 3, 5, and cannot prove the criterion of existence of chaos in second-order averaged system under quasi-periodic perturbation for ω 2 = nω 1 + εν, n = 2, 4, 6, 7, 8, 9, 10, 11, 12, where ν is not rational to ω 1 , but can show the occurrence of chaos in original system by numerical simulation. Numerical simulations including heteroclinic and homoclinic bifurcation surfaces, bifurcation diagrams, maximum Lyapunov exponents and Poincare map are given to illustrate the theoretical analysis, and to expose the more new complex dynamical behaviors. We show that cascades of period-doubling bifurcations from period-one to four orbits, cascades of interlocking period-doubling bifurcations from period-two orbits of two sets, from quasi-periodicity leading to chaos, onset of chaos which occurs more than one, interleaving occurrences of chaotic behavior and invariant torus, transient chaos with complex period windows and interior crisis, chaos converting to torus, different kind of chaotic attractors. Our results shows that the dynamical behaviors are different from the dynamics of duffing equation with two-well and two external forcings

  13. Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

    Science.gov (United States)

    Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

    2018-06-01

    We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

  14. The study of dynamic force acted on water strider leg departing from water surface

    Science.gov (United States)

    Sun, Peiyuan; Zhao, Meirong; Jiang, Jile; Zheng, Yelong

    2018-01-01

    Water-walking insects such as water striders can skate on the water surface easily with the help of the hierarchical structure on legs. Numerous theoretical and experimental studies show that the hierarchical structure would help water strider in quasi-static case such as load-bearing capacity. However, the advantage of the hierarchical structure in the dynamic stage has not been reported yet. In this paper, the function of super hydrophobicity and the hierarchical structure was investigated by measuring the adhesion force of legs departing from the water surface at different lifting speed by a dynamic force sensor. The results show that the adhesion force decreased with the increase of lifting speed from 0.02 m/s to 0.4 m/s, whose mechanic is investigated by Energy analysis. In addition, it can be found that the needle shape setae on water strider leg can help them depart from water surface easily. Thus, it can serve as a starting point to understand how the hierarchical structure on the legs help water-walking insects to jump upward rapidly to avoid preying by other insects.

  15. Effects of the van der Waals Force on the Dynamics Performance for a Micro Resonant Pressure Sensor

    Directory of Open Access Journals (Sweden)

    Lizhong Xu

    2016-01-01

    Full Text Available The micro resonant pressure sensor outputs the frequency signals where the distortion does not take place in a long distance transmission. As the dimensions of the sensor decrease, the effects of the van der Waals forces should be considered. Here, a coupled dynamic model of the micro resonant pressure sensor is proposed and its coupled dynamic equation is given in which the van der Waals force is considered. By the equation, the effects of the van der Waals force on the natural frequencies and vibration amplitudes of the micro resonant pressure sensor are investigated. Results show that the natural frequency and the vibrating amplitudes of the micro resonant pressure sensor are affected significantly by van der Waals force for a small clearance between the film and the base plate, a small initial tension stress of the film, and some other conditions.

  16. Resonant acoustic spectroscopy of soft tissues using embedded magnetomotive nanotransducers and optical coherence tomography

    International Nuclear Information System (INIS)

    Oldenburg, Amy L; Boppart, Stephen A

    2010-01-01

    We present a new method for performing dynamic elastography of soft tissue samples. By sensing nanoscale displacements with optical coherence tomography, a chirped, modulated force is applied to acquire the mechanical spectrum of a tissue sample within a few seconds. This modulated force is applied via magnetic nanoparticles, named 'nanotransducers', which are diffused into the tissue, and which contribute negligible inertia to the soft tissue mechanical system. Using this novel system, we observed that excised tissues exhibit mechanical resonance modes which are well described by a linear damped harmonic oscillator. Results are validated by using cylindrical tissue phantoms of agarose in which resonant frequencies (30-400 Hz) are consistent with longitudinal modes and the sample boundary conditions. We furthermore show that the Young's modulus can be computed from their measured resonance frequencies, analogous to resonant ultrasound spectroscopy for stiff material analysis. Using this new technique, named magnetomotive resonant acoustic spectroscopy (MRAS), we monitored the relative stiffening of an excised rat liver during a chemical fixation process.

  17. Implementing Molecular Dynamics for Hybrid High Performance Computers - 1. Short Range Forces

    International Nuclear Information System (INIS)

    Brown, W. Michael; Wang, Peng; Plimpton, Steven J.; Tharrington, Arnold N.

    2011-01-01

    The use of accelerators such as general-purpose graphics processing units (GPGPUs) have become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high performance computers, machines with more than one type of floating-point processor, are now becoming more prevalent due to these advantages. In this work, we discuss several important issues in porting a large molecular dynamics code for use on parallel hybrid machines - (1) choosing a hybrid parallel decomposition that works on central processing units (CPUs) with distributed memory and accelerator cores with shared memory, (2) minimizing the amount of code that must be ported for efficient acceleration, (3) utilizing the available processing power from both many-core CPUs and accelerators, and (4) choosing a programming model for acceleration. We present our solution to each of these issues for short-range force calculation in the molecular dynamics package LAMMPS. We describe algorithms for efficient short range force calculation on hybrid high performance machines. We describe a new approach for dynamic load balancing of work between CPU and accelerator cores. We describe the Geryon library that allows a single code to compile with both CUDA and OpenCL for use on a variety of accelerators. Finally, we present results on a parallel test cluster containing 32 Fermi GPGPUs and 180 CPU cores.

  18. Pico-second laser spectroscopy and reaction dynamics in liquids

    International Nuclear Information System (INIS)

    Mialocq, Jean-Claude

    1984-01-01

    The dynamic relaxation of excited singlet states of molecules and ions in liquid solution is investigated using picosecond laser spectroscopy. The more efficient process for the deactivation of the first excited singlet state of pinacyanol is internal conversion S 1 → S 0 between iso-energetic states. At low viscosity, the rate constant is inversely proportional to the macroscopic viscosity and depends on the relaxation of the angle between the quinoline end groups around the polymethinic chain. Electron photodetachment by 265 nm excitation of the ferrocyanide and phenolate anions and photoionisation of neutral molecules, phenol, indole and tryptophan in polar solvents give rise to the solvated electron formation. The mono-or bi-photonic nature of the ejection process and the solvent relaxation around the excess electron are analyzed. (author) [fr

  19. Whole-Body Human Inverse Dynamics with Distributed Micro-Accelerometers, Gyros and Force Sensing

    Directory of Open Access Journals (Sweden)

    Claudia Latella

    2016-05-01

    Full Text Available Human motion tracking is a powerful tool used in a large range of applications that require human movement analysis. Although it is a well-established technique, its main limitation is the lack of estimation of real-time kinetics information such as forces and torques during the motion capture. In this paper, we present a novel approach for a human soft wearable force tracking for the simultaneous estimation of whole-body forces along with the motion. The early stage of our framework encompasses traditional passive marker based methods, inertial and contact force sensor modalities and harnesses a probabilistic computational technique for estimating dynamic quantities, originally proposed in the domain of humanoid robot control. We present experimental analysis on subjects performing a two degrees-of-freedom bowing task, and we estimate the motion and kinetics quantities. The results demonstrate the validity of the proposed method. We discuss the possible use of this technique in the design of a novel soft wearable force tracking device and its potential applications.

  20. Atomic force and shear force based tip-enhanced Raman spectroscopy and imaging

    NARCIS (Netherlands)

    Kharintsev, S.S.; Hoffmann, G.G.; Dorozhkin, P.S.; With, de G.; Loos, J.

    2007-01-01

    Underlying near-field optibal effects on the nanoscale have stimulated the development of apertureless vibrational spectroscopy and imaging with ultrahigh spatial resolution. We demonstrate tip-enhanced Raman spectra of single-walled carbon nanotubes (SWCNTs), recorded with a scanning near-field

  1. Study of the Bulk Charge Carrier Dynamics in Anatase and Rutile TiO2 Single Crystals by Femtosecond Time Resolved Spectroscopy

    KAUST Repository

    Maity, Partha; Mohammed, Omar F.; Katsiev, Khabiboulakh; Idriss, Hicham

    2018-01-01

    as the best model for fundamental studies. Their ultrafast charge carrier dynamics especially on TiO2 anatase single crystal (the most active phase) are unresolved. Here femtosecond time resolved spectroscopy (TRS) was carried out to explore the dynamics

  2. Computational Intelligence Based Data Fusion Algorithm for Dynamic sEMG and Skeletal Muscle Force Modelling

    Energy Technology Data Exchange (ETDEWEB)

    Chandrasekhar Potluri,; Madhavi Anugolu; Marco P. Schoen; D. Subbaram Naidu

    2013-08-01

    In this work, an array of three surface Electrography (sEMG) sensors are used to acquired muscle extension and contraction signals for 18 healthy test subjects. The skeletal muscle force is estimated using the acquired sEMG signals and a Non-linear Wiener Hammerstein model, relating the two signals in a dynamic fashion. The model is obtained from using System Identification (SI) algorithm. The obtained force models for each sensor are fused using a proposed fuzzy logic concept with the intent to improve the force estimation accuracy and resilience to sensor failure or misalignment. For the fuzzy logic inference system, the sEMG entropy, the relative error, and the correlation of the force signals are considered for defining the membership functions. The proposed fusion algorithm yields an average of 92.49% correlation between the actual force and the overall estimated force output. In addition, the proposed fusionbased approach is implemented on a test platform. Experiments indicate an improvement in finger/hand force estimation.

  3. Vehicle Dynamics Control of In-wheel Electric Motor Drive Vehicles Based on Averaging of Tire Force Usage

    Science.gov (United States)

    Masaki, Nobuo; Iwano, Haruo; Kamada, Takayoshi; Nagai, Masao

    For in-wheel electric motor drive vehicles, a new vehicle dynamics control which is based on the tire force usage rate is proposed. The new controller adopts non-linear optimal control could manage the interference between direct yaw-moment control and the tire force usage rate. The new control is considered total longitudinal and transverse tire force. Therefore the controller can prevent tire force saturation near tire force limit during cornering. Simulations and test runs by the custom made four wheel drive in-wheel motor electric vehicle show that higher driving stability performance compared to the performance of the same vehicle without control.

  4. STUDY OF STATIC AND DYNAMIC STABILITY OF THIN-WALLED BARS EXCITED BY PERIODICAL AXIAL EXTERNAL FORCES.

    Directory of Open Access Journals (Sweden)

    Minodora Maria PASĂRE

    2010-10-01

    Full Text Available In these paper, starting from the relations for the displacements and spinning the transversal section of a bar with thin walls of sections opened expressed by the corresponding influence functions and introducing the components of the exterior forces distributed and the moments of the exterior forces distributed due to the inertia forces, the exciting axial forces together with the following effect of these and of the reaction forces of the elastic environment for leaning it may reach to the system of the equations of parametric vibrations under the form of three integral equation These equations may serve for the study of vibrations of the bars, to study the static stability and to study the dynamic stability

  5. Nonlinear dynamic response of cantilever beam tip during atomic force microscopy (AFM) nanolithography of copper surface

    International Nuclear Information System (INIS)

    Yeh, Y-L; Jang, M-J; Wang, C-C; Lin, Y-P; Chen, K-S

    2008-01-01

    This paper investigates the nonlinear dynamic response of an atomic force microscope (AFM) cantilever beam tip during the nanolithography of a copper (Cu) surface using a high-depth feed. The dynamic motion of the tip is modeled using a combined approach based on Newton's law and empirical observations. The cutting force is determined from experimental observations of the piling height on the Cu surface and the rotation angle of the cantilever beam tip. It is found that the piling height increases linearly with the cantilever beam carrier velocity. Furthermore, the cantilever beam tip is found to execute a saw tooth motion. Both this motion and the shear cutting force are nonlinear. The elastic modulus in the y direction is variable. Finally, the velocity of the cantilever beam tip as it traverses the specimen surface has a discrete characteristic rather than a smooth, continuous profile

  6. Droplet spreading driven by van der Waals force: a molecular dynamics study

    KAUST Repository

    Wu, Congmin

    2010-07-07

    The dynamics of droplet spreading is investigated by molecular dynamics simulations for two immiscible fluids of equal density and viscosity. All the molecular interactions are modeled by truncated Lennard-Jones potentials and a long-range van der Waals force is introduced to act on the wetting fluid. By gradually increasing the coupling constant in the attractive van der Waals interaction between the wetting fluid and the substrate, we observe a transition in the initial stage of spreading. There exists a critical value of the coupling constant, above which the spreading is pioneered by a precursor film. In particular, the dynamically determined critical value quantitatively agrees with that determined by the energy criterion that the spreading coefficient equals zero. The latter separates partial wetting from complete wetting. In the regime of complete wetting, the radius of the spreading droplet varies with time as R(t) ∼ √t, a behavior also found in molecular dynamics simulations where the wetting dynamics is driven by the short-range Lennard-Jones interaction between liquid and solid. © 2010 IOP Publishing Ltd.

  7. Single-cell force spectroscopy as a technique to quantify human red blood cell adhesion to subendothelial laminin.

    Science.gov (United States)

    Maciaszek, Jamie L; Partola, Kostyantyn; Zhang, Jing; Andemariam, Biree; Lykotrafitis, George

    2014-12-18

    Single-cell force spectroscopy (SCFS), an atomic force microscopy (AFM)-based assay, enables quantitative study of cell adhesion while maintaining the native state of surface receptors in physiological conditions. Human healthy and pathological red blood cells (RBCs) express a large number of surface proteins which mediate cell-cell interactions, or cell adhesion to the extracellular matrix. In particular, RBCs adhere with high affinity to subendothelial matrix laminin via the basal cell adhesion molecule and Lutheran protein (BCAM/Lu). Here, we established SCFS as an in vitro technique to study human RBC adhesion at baseline and following biochemical treatment. Using blood obtained from healthy human subjects, we recorded adhesion forces from single RBCs attached to AFM cantilevers as the cell was pulled-off of substrates coated with laminin protein. We found that an increase in the overall cell adhesion measured via SCFS is correlated with an increase in the resultant total force measured on 1 µm(2) areas of the RBC membrane. Further, we showed that SCFS can detect significant changes in the adhesive response of RBCs to modulation of the cyclic adenosine monophosphate (cAMP) and protein kinase A (PKA) pathway. Lastly, we identified variability in the RBC adhesion force to laminin amongst the human subjects, suggesting that RBCs maintain diverse levels of active BCAM/Lu adhesion receptors. By using single-cell measurements, we established a powerful new method for the quantitative measurement of single RBC adhesion with specific receptor-mediated binding. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. Optimal design of a vehicle magnetorheological damper considering the damping force and dynamic range

    International Nuclear Information System (INIS)

    Nguyen, Quoc-Hung; Choi, Seung-Bok

    2009-01-01

    This paper presents an optimal design of a passenger vehicle magnetorheological (MR) damper based on finite element analysis. The MR damper is constrained in a specific volume and the optimization problem identifies the geometric dimensions of the damper that minimize an objective function. The objective function consists of the damping force, the dynamic range, and the inductive time constant of the damper. After describing the configuration of the MR damper, the damping force and dynamic range are obtained on the basis of the Bingham model of an MR fluid. Then, the control energy (power consumption of the damper coil) and the inductive time constant are derived. The objective function for the optimization problem is determined based on the solution of the magnetic circuit of the initial damper. Subsequently, the optimization procedure, using a golden-section algorithm and a local quadratic fitting technique, is constructed via commercial finite element method parametric design language. Using the developed optimization tool, optimal solutions of the MR damper, which are constrained in a specific cylindrical volume defined by its radius and height, are determined and a comparative work on damping force and inductive time constant between the initial and optimal design is undertaken

  9. The study of dynamic force acted on water strider leg departing from water surface

    Directory of Open Access Journals (Sweden)

    Peiyuan Sun

    2018-01-01

    Full Text Available Water-walking insects such as water striders can skate on the water surface easily with the help of the hierarchical structure on legs. Numerous theoretical and experimental studies show that the hierarchical structure would help water strider in quasi-static case such as load-bearing capacity. However, the advantage of the hierarchical structure in the dynamic stage has not been reported yet. In this paper, the function of super hydrophobicity and the hierarchical structure was investigated by measuring the adhesion force of legs departing from the water surface at different lifting speed by a dynamic force sensor. The results show that the adhesion force decreased with the increase of lifting speed from 0.02 m/s to 0.4 m/s, whose mechanic is investigated by Energy analysis. In addition, it can be found that the needle shape setae on water strider leg can help them depart from water surface easily. Thus, it can serve as a starting point to understand how the hierarchical structure on the legs help water-walking insects to jump upward rapidly to avoid preying by other insects.

  10. Ultrafast Dynamics in Light-Driven Molecular Rotary Motors Probed by Femtosecond Stimulated Raman Spectroscopy

    NARCIS (Netherlands)

    Hall, Christopher R.; Conyard, Jamie; Heisler, Ismael A.; Jones, Garth; Frost, James; Browne, Wesley R.; Feringa, Ben L.; Meech, Stephen R.

    2017-01-01

    Photochemical isomerization in sterically crowded chiral alkenes is the driving force for molecular rotary motors in nanoscale machines. Here the excited-state dynamics and structural evolution of the prototypical light-driven rotary motor are followed on the ultrafast time scale by femtosecond

  11. Development of force sensing circuit to determine the optimal force required for effective dynamic tripod grip/writing

    Science.gov (United States)

    Suraj S., S.; Kulkarni, Palash; Bokadia, Pratik; Ramanathan, Prabhu; Nageswaran, Sharmila

    2018-04-01

    Handwriting is a combination of fine motor perceptions and cognitive skills to produce words on paper. For writing, the most commonly used and recommended grip is the dynamic tripod grip. A child's handwriting starts developing during the times of pre-schooling and improves over time. While writing, children apply excessive force on the writing instrument. This force is exerted by their fingers and as per the law of reaction, the writing instruments tend to exert an equal and opposite force, that could damage the delicate soft tissue structures in their fingers and initiate cramps and pains. This condition is also prevalent in adults who tend to write for long hours under pressure. An example would be adolescence student during the exams. Clinically this condition is termed as `Writer's Cramp', which is usually characterized by muscle fatigue and pain in the fingers. By understanding and fixing the threshold of the force that should be exerted by the fingers while gripping the instrument, the pain can be controlled or avoided. This research aims in designing an electronic module which can help in understanding the threshold of pressure which is optimum enough to establish a better contact between the fingers and the instrument and should be capable of controlling or avoiding the pain. The design of FSR based electronic system is explained with its circuitry and results of initial testing is presented in this paper.

  12. Ultrafast pre-breakdown dynamics in Al₂O₃SiO₂ reflector by femtosecond UV laser spectroscopy.

    Science.gov (United States)

    Du, Juan; Li, Zehan; Xue, Bing; Kobayashi, Takayoshi; Han, Dongjia; Zhao, Yuanan; Leng, Yuxin

    2015-06-29

    Ultrafast carrier dynamics in Al2O3/SiO2 high reflectors has been investigated by UV femtosecond laser. It is identified by laser spectroscopy that, the carrier dynamics contributed from the front few layers of Al2O3 play a dominating role in the initial laser-induced damage of the UV reflector. Time-resolved reflection decrease after the UV excitation is observed, and conduction electrons is found to relaxed to a mid-gap defect state locating about one photon below the conduction band . To interpret the laser induced carrier dynamics further, a theoretical model including electrons relaxation to a mid-gap state is built, and agrees very well with the experimental results.. To the best of our knowledge, this is the first study on the pre-damage dynamics in UV high reflector induced by femtosecond UV laser.

  13. Dynamic simulation of knee-joint loading during gait using force-feedback control and surrogate contact modelling.

    Science.gov (United States)

    Walter, Jonathan P; Pandy, Marcus G

    2017-10-01

    The aim of this study was to perform multi-body, muscle-driven, forward-dynamics simulations of human gait using a 6-degree-of-freedom (6-DOF) model of the knee in tandem with a surrogate model of articular contact and force control. A forward-dynamics simulation incorporating position, velocity and contact force-feedback control (FFC) was used to track full-body motion capture data recorded for multiple trials of level walking and stair descent performed by two individuals with instrumented knee implants. Tibiofemoral contact force errors for FFC were compared against those obtained from a standard computed muscle control algorithm (CMC) with a 6-DOF knee contact model (CMC6); CMC with a 1-DOF translating hinge-knee model (CMC1); and static optimization with a 1-DOF translating hinge-knee model (SO). Tibiofemoral joint loads predicted by FFC and CMC6 were comparable for level walking, however FFC produced more accurate results for stair descent. SO yielded reasonable predictions of joint contact loading for level walking but significant differences between model and experiment were observed for stair descent. CMC1 produced the least accurate predictions of tibiofemoral contact loads for both tasks. Our findings suggest that reliable estimates of knee-joint loading may be obtained by incorporating position, velocity and force-feedback control with a multi-DOF model of joint contact in a forward-dynamics simulation of gait. Copyright © 2017 IPEM. Published by Elsevier Ltd. All rights reserved.

  14. On the dynamics of polymers in dense systems - Results of neutron spin echo spectroscopy

    International Nuclear Information System (INIS)

    Richter, D.

    1997-01-01

    One of the basic problems in the dynamics of polymers concerns the importance of geometrical or topological interactions which are directly related to the large scale molecular structures. In the famous reptation model these constraints are pictured in terms of a tube of localization following the average chain profile and confining the chain motion to the curve-linear tube. Recently studying the dynamic structure factor of a single labeled chain in a polymer melt by means of neutron spin echo spectroscopy (NSE) led to a direct observation of these tube constraints. Here I shall summarize these neutron spin echo experiments. I shall address the NSE technique, present results on the entropy driven segmental chain dynamics, discuss the dynamics of single chains in the melt where the chain length is increased through the transition to 'reptation' dynamics and display NSE measurements on long chain systems which revealed the molecular existence of the entanglement distance. Their magnitudes agree very well with tube diameters derived from dynamical mechanical measurements on the basis of the reptation model proving thereby the basic assumption of this Nobel Price winning concept

  15. Nonlinear dynamics of a thin liquid film on an axially oscillating cylindrical surface subjected to double-frequency forcing.

    Science.gov (United States)

    Haimovich, Ory; Oron, Alexander

    2013-05-01

    The nonlinear dynamics of a thin axisymmetric liquid film on a horizontal cylindrical substrate subjected to an axial double-frequency forcing that consists of two components of different amplitudes and frequencies and a possible phase shift is considered in this paper. A nonlinear evolution equation governing the spatiotemporal dynamics of the film interface has been derived in the long-wave limit. Similar to the case of a single-frequency forcing considered in our earlier work, there exists a critical forcing amplitude below which the film undergoes a long-time capillary rupture typical for a static cylinder, whereas above it the film remains continuous. We find that it is possible to arrest the rupture even if the forcing parameters of each of the two components correspond separately to the domain where rupture takes place. It is shown that the critical forcing amplitude is easily determined via a single-frequency case when the two forcing frequencies are equal. In the case of different forcing amplitudes and frequencies, the variation of the critical forcing amplitude as a function of the frequency ratio exhibits a unique behavior displaying the emergence of spikes. A related case of an amplitude-modulated single-frequency forcing is also addressed here. For a sufficiently small frequency of the amplitude modulation, a significant increase of the pattern amplitude is observed. In the case of commensurate forcing frequencies, the flow is found to be quasiperiodic.

  16. Vibrations of bioionic liquids by ab initio molecular dynamics and vibrational spectroscopy.

    Science.gov (United States)

    Tanzi, Luana; Benassi, Paola; Nardone, Michele; Ramondo, Fabio

    2014-12-26

    Density functional theory and vibrational spectroscopy are used to investigate a class of bioionic liquids consisting of a choline cation and carboxylate anions. Through quantum mechanical studies of motionless ion pairs and molecular dynamics of small portions of the liquid, we have characterized important structural features of the ionic liquid. Hydrogen bonding produces stable ion pairs in the liquid and induces vibrational features of the carboxylate groups comparable with experimental results. Infrared and Raman spectra of liquids have been measured, and main bands have been assigned on the basis of theoretical spectra.

  17. Photo-initiated dynamics and spectroscopy of the deprotonated Green Fluorescent Protein chromophore

    DEFF Research Database (Denmark)

    Bochenkova, Anastasia; Andersen, Lars Henrik

    2013-01-01

    . Knowledge of intrinsic properties of the GFP photoabsorbing molecular unit is a prerequisite in understanding the atomic-scale interactions that play a key role for the diverse functioning of these proteins. Here, we show how recent developments in action and photoelectron spectroscopy combined with state...... efficiently compete with each other in spite of their inherently different intrinsic timescales. The reason behind this is an efficient coupling between the nuclear and electronic motion in the photo-initiated dynamics, where the energy may be transferred from nuclei to electrons and from electrons to nuclei...

  18. Multiplexed single-molecule force spectroscopy using a centrifuge.

    Science.gov (United States)

    Yang, Darren; Ward, Andrew; Halvorsen, Ken; Wong, Wesley P

    2016-03-17

    We present a miniature centrifuge force microscope (CFM) that repurposes a benchtop centrifuge for high-throughput single-molecule experiments with high-resolution particle tracking, a large force range, temperature control and simple push-button operation. Incorporating DNA nanoswitches to enable repeated interrogation by force of single molecular pairs, we demonstrate increased throughput, reliability and the ability to characterize population heterogeneity. We perform spatiotemporally multiplexed experiments to collect 1,863 bond rupture statistics from 538 traceable molecular pairs in a single experiment, and show that 2 populations of DNA zippers can be distinguished using per-molecule statistics to reduce noise.

  19. Measurement correction method for force sensor used in dynamic pressure calibration based on artificial neural network optimized by genetic algorithm

    Science.gov (United States)

    Gu, Tingwei; Kong, Deren; Shang, Fei; Chen, Jing

    2017-12-01

    We present an optimization algorithm to obtain low-uncertainty dynamic pressure measurements from a force-transducer-based device. In this paper, the advantages and disadvantages of the methods that are commonly used to measure the propellant powder gas pressure, the applicable scope of dynamic pressure calibration devices, and the shortcomings of the traditional comparison calibration method based on the drop-weight device are firstly analysed in detail. Then, a dynamic calibration method for measuring pressure using a force sensor based on a drop-weight device is introduced. This method can effectively save time when many pressure sensors are calibrated simultaneously and extend the life of expensive reference sensors. However, the force sensor is installed between the drop-weight and the hammerhead by transition pieces through the connection mode of bolt fastening, which causes adverse effects such as additional pretightening and inertia forces. To solve these effects, the influence mechanisms of the pretightening force, the inertia force and other influence factors on the force measurement are theoretically analysed. Then a measurement correction method for the force measurement is proposed based on an artificial neural network optimized by a genetic algorithm. The training and testing data sets are obtained from calibration tests, and the selection criteria for the key parameters of the correction model is discussed. The evaluation results for the test data show that the correction model can effectively improve the force measurement accuracy of the force sensor. Compared with the traditional high-accuracy comparison calibration method, the percentage difference of the impact-force-based measurement is less than 0.6% and the relative uncertainty of the corrected force value is 1.95%, which can meet the requirements of engineering applications.

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

    Science.gov (United States)

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

    2010-10-07

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

  1. Stochastic modeling of lift and drag dynamics to obtain aerodynamic forces with local dynamics on rotor blade under unsteady wind inflow

    International Nuclear Information System (INIS)

    Luhur, M.R.

    2014-01-01

    This contribution provides the development of a stochastic lift and drag model for an airfoil FX 79-W-151A under unsteady wind inflow based on wind tunnel measurements. Here we present the integration of the stochastic model into a well-known standard BEM (Blade Element Momentum) model to obtain the corresponding aerodynamic forces on a rotating blade element. The stochastic model is integrated as an alternative to static tabulated data used by classical BEM. The results show that in comparison to classical BEM, the BEM with stochastic approach additionally reflects the local force dynamics and therefore provides more information on aerodynamic forces that can be used by wind turbine simulation codes. (author)

  2. Stochastic Modeling of Lift and Drag Dynamics to Obtain Aerodynamic Forces with Local Dynamics on Rotor Blade under Unsteady Wind Inflow

    Directory of Open Access Journals (Sweden)

    Muhammad Ramzan Luhur

    2014-01-01

    Full Text Available This contribution provides the development of a stochastic lift and drag model for an airfoil FX 79-W-151A under unsteady wind inflow based on wind tunnel measurements. Here we present the integration of the stochastic model into a well-known standard BEM (Blade Element Momentum model to obtain the corresponding aerodynamic forces on a rotating blade element. The stochastic model is integrated as an alternative to static tabulated data used by classical BEM. The results show that in comparison to classical BEM, the BEM with stochastic approach additionally reflects the local force dynamics and therefore provides more information on aerodynamic forces that can be used by wind turbine simulation codes

  3. Single-order laser high harmonics in XUV for ultrafast photoelectron spectroscopy of molecular wavepacket dynamics

    Directory of Open Access Journals (Sweden)

    Mizuho Fushitani

    2016-11-01

    Full Text Available We present applications of extreme ultraviolet (XUV single-order laser harmonics to gas-phase ultrafast photoelectron spectroscopy. Ultrashort XUV pulses at 80 nm are obtained as the 5th order harmonics of the fundamental laser at 400 nm by using Xe or Kr as the nonlinear medium and separated from other harmonic orders by using an indium foil. The single-order laser harmonics is applied for real-time probing of vibrational wavepacket dynamics of I2 molecules in the bound and dissociating low-lying electronic states and electronic-vibrational wavepacket dynamics of highly excited Rydberg N2 molecules.

  4. Single-order laser high harmonics in XUV for ultrafast photoelectron spectroscopy of molecular wavepacket dynamics.

    Science.gov (United States)

    Fushitani, Mizuho; Hishikawa, Akiyoshi

    2016-11-01

    We present applications of extreme ultraviolet (XUV) single-order laser harmonics to gas-phase ultrafast photoelectron spectroscopy. Ultrashort XUV pulses at 80 nm are obtained as the 5th order harmonics of the fundamental laser at 400 nm by using Xe or Kr as the nonlinear medium and separated from other harmonic orders by using an indium foil. The single-order laser harmonics is applied for real-time probing of vibrational wavepacket dynamics of I 2 molecules in the bound and dissociating low-lying electronic states and electronic-vibrational wavepacket dynamics of highly excited Rydberg N 2 molecules.

  5. Dynamic cerebral autoregulation measured with coherent hemodynamics spectroscopy (CHS)

    Science.gov (United States)

    Kainerstorfer, Jana M.; Sassaroli, Angelo; Tgavalekos, Kristen T.; Fantini, Sergio

    2015-03-01

    Coherent Hemodynamics Spectroscopy (CHS) is a novel technique for non-invasive measurements of local microcirculation quantities such as the capillary blood transit times and dynamic autoregulation. The basis of CHS is to measure, for instance with near-infrared spectroscopy (NIRS), peripheral coherent hemodynamic changes that are induced by controlled perturbations in the systemic mean arterial pressure (MAP). In this study, the MAP perturbation was induced by the fast release of two pneumatic cuffs placed around the subject's thighs after they were kept inflated (at 200 mmHg) for two minutes. The resulting transient changes in cerebral oxy- (O) and deoxy- (D) hemoglobin concentrations measured with NIRS on the prefrontal cortex are then described by a novel hemodynamic model, from which quantifiable parameters such as the capillary blood transit time and a cutoff frequency for cerebral autoregulation are obtained. We present results on eleven healthy volunteers in a protocol involving measurements during normal breathing and during hyperventilation, which is known to cause a hypocapnia-induced increase in cerebral autoregulation. The measured capillary transit time was unaffected by hyperventilation (normal breathing: 1.1±0.1 s; hyperventilation: 1.1±0.1 s), whereas the cutoff frequency of autoregulation, which increases for higher autoregulation efficiency, was indeed found to be significantly greater during hyperventilation (normal breathing: 0.017±0.002 Hz; hyperventilation: 0.034±0.005 Hz). These results provide a validation of local cerebral autoregulation measurements with the new technique of CHS.

  6. Ultrafast X-Ray Spectroscopy of Conical Intersections

    Science.gov (United States)

    Neville, Simon P.; Chergui, Majed; Stolow, Albert; Schuurman, Michael S.

    2018-06-01

    Ongoing developments in ultrafast x-ray sources offer powerful new means of probing the complex nonadiabatically coupled structural and electronic dynamics of photoexcited molecules. These non-Born-Oppenheimer effects are governed by general electronic degeneracies termed conical intersections, which play a key role, analogous to that of a transition state, in the electronic-nuclear dynamics of excited molecules. Using high-level ab initio quantum dynamics simulations, we studied time-resolved x-ray absorption (TRXAS) and photoelectron spectroscopy (TRXPS) of the prototypical unsaturated organic chromophore, ethylene, following excitation to its S2(π π*) state. The TRXAS, in particular, is highly sensitive to all aspects of the ensuing dynamics. These x-ray spectroscopies provide a clear signature of the wave packet dynamics near conical intersections, related to charge localization effects driven by the nuclear dynamics. Given the ubiquity of charge localization in excited state dynamics, we believe that ultrafast x-ray spectroscopies offer a unique and powerful route to the direct observation of dynamics around conical intersections.

  7. Control of dynamical self-assembly of strongly Brownian nanoparticles through convective forces induced by ultrafast laser

    Science.gov (United States)

    Ilday, Serim; Akguc, Gursoy B.; Tokel, Onur; Makey, Ghaith; Yavuz, Ozgun; Yavuz, Koray; Pavlov, Ihor; Ilday, F. Omer; Gulseren, Oguz

    We report a new dynamical self-assembly mechanism, where judicious use of convective and strong Brownian forces enables effective patterning of colloidal nanoparticles that are almost two orders of magnitude smaller than the laser beam. Optical trapping or tweezing effects are not involved, but the laser is used to create steep thermal gradients through multi-photon absorption, and thereby guide the colloids through convective forces. Convective forces can be thought as a positive feedback mechanism that helps to form and reinforce pattern, while Brownian motion act as a competing negative feedback mechanism to limit the growth of the pattern, as well as to increase the possibilities of bifurcation into different patterns, analogous to the competition observed in reaction-diffusion systems. By steering stochastic processes through these forces, we are able to gain control over the emergent pattern such as to form-deform-reform of a pattern, to change its shape and transport it spatially within seconds. This enables us to dynamically initiate and control large patterns comprised of hundreds of colloids. Further, by not relying on any specific chemical, optical or magnetic interaction, this new method is, in principle, completely independent of the material type being assembled.

  8. A new method for measuring lift forces acting on an airfoil under dynamic conditions

    Energy Technology Data Exchange (ETDEWEB)

    Wolken-Moehlmann, Gerrit; Peinke, Joachim [Institute of Physics, University of Oldenburg (Germany)

    2008-07-01

    Wind turbines operate in a turbulent atmospheric boundary layer and are exposed to strong wind fluctuations in time and space. This can induce the dynamic stall, a phenomenon that causes extra loads. Dynamic stall occurs under fast changes in the angle of attack (AoA) and was determined in detail in helicopter research. But in contrast to helicopter aerodynamics, the changes in the AoA of wind turbine airfoils are in general non-sinusoidal, and thus it seems to be difficult to use these measurements and models. Our goal is to acquire lift data under conditions more comparable to real wind turbines, including non-periodic changes in the AoA. For this purpose a closed test section for our wind tunnel was built. An airfoil with a chord length of 0.2m will be rotated by a stepping motor with angular velocities of up to 300 {sup circle} /s. With a maximum wind velocity of 50m/s, Reynolds numbers of Re=700 000 can be realized. The lift force is determined by the counter forces acting on the wind tunnel walls. These are measured by two lines of 40 pressure sensors with sampling rates up to 2kHz. The results show distinct dynamic stall characteristics. Further experiments with different parameters and foils will give a better insight in dynamic stall and a verification and improvement of existing models.

  9. Calculation of dynamic hydraulic forces in nuclear plant piping systems

    International Nuclear Information System (INIS)

    Choi, D.K.

    1982-01-01

    A computer code was developed as one of the tools needed for analysis of piping dynamic loading on nuclear power plant high energy piping systems, including reactor safety and relief value upstream and discharge piping systems. The code calculates the transient hydraulic data and dynamic forces within the one-dimensional system, caused by a pipe rupture or sudden value motion, using a fixed space and varying time grid-method of characteristics. Subcooled, superheated, homogeneous two-phase and transition flow regimes are considered. A non-equilibrium effect is also considered in computing the fluid specific volume and fluid local sonic velocity in the two-phase mixture. Various hydraulic components such as a spring loaded or power operated value, enlarger, orifice, pressurized tank, multiple pipe junction (tee), etc. are considered as boundary conditions. Comparisons of calculated results with available experimental data shows a good agreement. (Author)

  10. 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.

  11. Quantifying non-ergodic dynamics of force-free granular gases.

    Science.gov (United States)

    Bodrova, Anna; Chechkin, Aleksei V; Cherstvy, Andrey G; Metzler, Ralf

    2015-09-14

    Brownian motion is ergodic in the Boltzmann-Khinchin sense that long time averages of physical observables such as the mean squared displacement provide the same information as the corresponding ensemble average, even at out-of-equilibrium conditions. This property is the fundamental prerequisite for single particle tracking and its analysis in simple liquids. We study analytically and by event-driven molecular dynamics simulations the dynamics of force-free cooling granular gases and reveal a violation of ergodicity in this Boltzmann-Khinchin sense as well as distinct ageing of the system. Such granular gases comprise materials such as dilute gases of stones, sand, various types of powders, or large molecules, and their mixtures are ubiquitous in Nature and technology, in particular in Space. We treat-depending on the physical-chemical properties of the inter-particle interaction upon their pair collisions-both a constant and a velocity-dependent (viscoelastic) restitution coefficient ε. Moreover we compare the granular gas dynamics with an effective single particle stochastic model based on an underdamped Langevin equation with time dependent diffusivity. We find that both models share the same behaviour of the ensemble mean squared displacement (MSD) and the velocity correlations in the limit of weak dissipation. Qualitatively, the reported non-ergodic behaviour is generic for granular gases with any realistic dependence of ε on the impact velocity of particles.

  12. New force replica exchange method and protein folding pathways probed by force-clamp technique.

    Science.gov (United States)

    Kouza, Maksim; Hu, Chin-Kun; Li, Mai Suan

    2008-01-28

    We have developed a new extended replica exchange method to study thermodynamics of a system in the presence of external force. Our idea is based on the exchange between different force replicas to accelerate the equilibrium process. This new approach was applied to obtain the force-temperature phase diagram and other thermodynamical quantities of the three-domain ubiquitin. Using the C(alpha)-Go model and the Langevin dynamics, we have shown that the refolding pathways of single ubiquitin depend on which terminus is fixed. If the N end is fixed then the folding pathways are different compared to the case when both termini are free, but fixing the C terminal does not change them. Surprisingly, we have found that the anchoring terminal does not affect the pathways of individual secondary structures of three-domain ubiquitin, indicating the important role of the multidomain construction. Therefore, force-clamp experiments, in which one end of a protein is kept fixed, can probe the refolding pathways of a single free-end ubiquitin if one uses either the polyubiquitin or a single domain with the C terminus anchored. However, it is shown that anchoring one end does not affect refolding pathways of the titin domain I27, and the force-clamp spectroscopy is always capable to predict folding sequencing of this protein. We have obtained the reasonable estimate for unfolding barrier of ubiquitin, using the microscopic theory for the dependence of unfolding time on the external force. The linkage between residue Lys48 and the C terminal of ubiquitin is found to have the dramatic effect on the location of the transition state along the end-to-end distance reaction coordinate, but the multidomain construction leaves the transition state almost unchanged. We have found that the maximum force in the force-extension profile from constant velocity force pulling simulations depends on temperature nonlinearly. However, for some narrow temperature interval this dependence becomes

  13. Comparison of nanoparticle diffusion using fluorescence correlation spectroscopy and differential dynamic microscopy within concentrated polymer solutions

    Science.gov (United States)

    Shokeen, Namita; Issa, Christopher; Mukhopadhyay, Ashis

    2017-12-01

    We studied the diffusion of nanoparticles (NPs) within aqueous entangled solutions of polyethylene oxide (PEO) by using two different optical techniques. Fluorescence correlation spectroscopy, a method widely used to investigate nanoparticle dynamics in polymer solution, was used to measure the long-time diffusion coefficient (D) of 25 nm radius particles within high molecular weight, Mw = 600 kg/mol PEO in water solutions. Differential dynamic microscopy (DDM) was used to determine the wave-vector dependent dynamics of NPs within the same polymer solutions. Our results showed good agreement between the two methods, including demonstration of normal diffusion and almost identical diffusion coefficients obtained by both techniques. The research extends the scope of DDM to study the dynamics and rheological properties of soft matter at a nanoscale. The measured diffusion coefficients followed a scaling theory, which can be explained by the coupling between polymer dynamics and NP motion.

  14. Simultaneous measurement of dynamic force and spatial thin film thickness between deformable and solid surfaces by integrated thin liquid film force apparatus.

    Science.gov (United States)

    Zhang, Xurui; Tchoukov, Plamen; Manica, Rogerio; Wang, Louxiang; Liu, Qingxia; Xu, Zhenghe

    2016-11-09

    Interactions involving deformable surfaces reveal a number of distinguishing physicochemical characteristics that do not exist in interactions between rigid solid surfaces. A unique fully custom-designed instrument, referred to as integrated thin liquid film force apparatus (ITLFFA), was developed to study the interactions between one deformable and one solid surface in liquid. Incorporating a bimorph force sensor with interferometry, this device allows for the simultaneous measurement of the time-dependent interaction force and the corresponding spatiotemporal film thickness of the intervening liquid film. The ITLFFA possesses the specific feature of conducting measurement under a wide range of hydrodynamic conditions, with a displacement velocity of deformable surfaces ranging from 2 μm s -1 to 50 mm s -1 . Equipped with a high speed camera, the results of a bubble interacting with hydrophilic and partially hydrophobic surfaces in aqueous solutions indicated that ITLFFA can provide information on interaction forces and thin liquid film drainage dynamics not only in a stable film but also in films of the quick rupture process. The weak interaction force was extracted from a measured film profile. Because of its well-characterized experimental conditions, ITLFFA permits the accurate and quantitative comparison/validation between measured and calculated interaction forces and temporal film profiles.

  15. Contact forces between a particle and a wet wall at both quasi-static and dynamic state

    Directory of Open Access Journals (Sweden)

    Zhang Huang

    2017-01-01

    Full Text Available The contact regime of particle-wall is investigated by the atomic force microscope (AFM and theoretical models. First, AFM is used to measure the cohesive force between a micron-sized grain and a glass plate at quasi-static state under various humidity. It is found out that the cohesive force starts to grow slowly and suddenly increase rapidly beyond a critical Relative Humidity (RH. Second, mathematical models of contacting forces are presented to depict the dynamic process that a particle impacts on a wet wall. Then the energy loss of a falling grain is calculated in comparison with the models and the experimental data from the previous references. The simulation results show that the force models presented here are adaptive for both low and high viscosity fluid films with different thickness.

  16. Excited state non-adiabatic dynamics of N-methylpyrrole: A time-resolved photoelectron spectroscopy and quantum dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Guorong [National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6 (Canada); State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023 (China); Synergetic Innovation Center of Quantum Information & Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Neville, Simon P. [Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5 (Canada); Schalk, Oliver [National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6 (Canada); Department of Physics, AlbaNova University Center, Stockholm University, Roslagstullsbacken 21, 106 91 Stockholm (Sweden); Sekikawa, Taro [Department of Applied Physics, Hokkaido University, Kita-13 Nishi-8, Kita-ku, Sapporo 060-8628 (Japan); Ashfold, Michael N. R. [School of Chemistry, University of Bristol, Bristol BS8 1TS (United Kingdom); Worth, Graham A. [School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT (United Kingdom); Stolow, Albert, E-mail: astolow@uottawa.ca [National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6 (Canada); Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5 (Canada); Department of Physics, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario K1N 6N5 (Canada)

    2016-01-07

    The dynamics of N-methylpyrrole following excitation at wavelengths in the range 241.5-217.0 nm were studied using a combination of time-resolved photoelectron spectroscopy (TRPES), ab initio quantum dynamics calculations using the multi-layer multi-configurational time-dependent Hartree method, as well as high-level photoionization cross section calculations. Excitation at 241.5 and 236.2 nm results in population of the A{sub 2}(πσ{sup ∗}) state, in agreement with previous studies. Excitation at 217.0 nm prepares the previously neglected B{sub 1}(π3p{sub y}) Rydberg state, followed by prompt internal conversion to the A{sub 2}(πσ{sup ∗}) state. In contrast with the photoinduced dynamics of pyrrole, the lifetime of the wavepacket in the A{sub 2}(πσ{sup ∗}) state was found to vary with excitation wavelength, decreasing by one order of magnitude upon tuning from 241.5 nm to 236.2 nm and by more than three orders of magnitude when excited at 217.0 nm. The order of magnitude difference in lifetimes measured at the longer excitation wavelengths is attributed to vibrational excitation in the A{sub 2}(πσ{sup ∗}) state, facilitating wavepacket motion around the potential barrier in the N–CH{sub 3} dissociation coordinate.

  17. Excited state non-adiabatic dynamics of N-methylpyrrole: A time-resolved photoelectron spectroscopy and quantum dynamics study

    International Nuclear Information System (INIS)

    Wu, Guorong; Neville, Simon P.; Schalk, Oliver; Sekikawa, Taro; Ashfold, Michael N. R.; Worth, Graham A.; Stolow, Albert

    2016-01-01

    The dynamics of N-methylpyrrole following excitation at wavelengths in the range 241.5-217.0 nm were studied using a combination of time-resolved photoelectron spectroscopy (TRPES), ab initio quantum dynamics calculations using the multi-layer multi-configurational time-dependent Hartree method, as well as high-level photoionization cross section calculations. Excitation at 241.5 and 236.2 nm results in population of the A 2 (πσ ∗ ) state, in agreement with previous studies. Excitation at 217.0 nm prepares the previously neglected B 1 (π3p y ) Rydberg state, followed by prompt internal conversion to the A 2 (πσ ∗ ) state. In contrast with the photoinduced dynamics of pyrrole, the lifetime of the wavepacket in the A 2 (πσ ∗ ) state was found to vary with excitation wavelength, decreasing by one order of magnitude upon tuning from 241.5 nm to 236.2 nm and by more than three orders of magnitude when excited at 217.0 nm. The order of magnitude difference in lifetimes measured at the longer excitation wavelengths is attributed to vibrational excitation in the A 2 (πσ ∗ ) state, facilitating wavepacket motion around the potential barrier in the N–CH 3 dissociation coordinate

  18. Complex dynamics in Josephson system with two external forcing terms

    International Nuclear Information System (INIS)

    Yang Jianping; Feng Wei; Jing Zhujun

    2006-01-01

    Josephson system with two external forcing terms is investigated. By applying Melnikov method, we prove that criterion of existence of chaos under periodic perturbation. By second-order averaging method and Melnikov method, we obtain the criterion of existence of chaos in averaged system under quasi-periodic perturbation for ω 2 =ω 1 +εν, and cannot prove the criterion of existence of chaos in averaged system under quasi-periodic perturbation for ω 2 =nω 1 +εν (n>=2 and n-bar N), where ν is not rational to ω 1 . We also study the effects of the parameters of system on dynamical behaviors by using numerical simulation. The numerical simulations, including bifurcation diagram of fixed points, bifurcation diagram of system in three- and two-dimensional space, homoclinic and heteroclinic bifurcation surface, Maximum Lyapunov exponent, phase portraits, Poincare map, are also plotted to illustrate theoretical analysis, and to expose the complex dynamical behaviors, including the period-n (n=1,2,5,7) orbits in different chaotic regions, cascades of period-doubling bifurcation from period-1, 2 and 5 orbits, reverse period-doubling bifurcation, onset of chaos which occurs more than once for two given external frequencies and chaos suddenly converting to periodic orbits, transient chaos with complex periodic windows and crisis, reverse period-5 bubble, non-attracting chaotic set and nice attracting chaotic set. In particular, we observe that the system can leave chaotic region to periodic motion by adjusting damping α, amplitude f 1 and frequency ω 2 of external forcing which can be considered as a control strategy

  19. Dynamic membrane interactions of antibacterial and antifungal biomolecules, and amyloid peptides, revealed by solid-state NMR spectroscopy.

    Science.gov (United States)

    Naito, Akira; Matsumori, Nobuaki; Ramamoorthy, Ayyalusamy

    2018-02-01

    A variety of biomolecules acting on the cell membrane folds into a biologically active structure in the membrane environment. It is, therefore, important to determine the structures and dynamics of such biomolecules in a membrane environment. While several biophysical techniques are used to obtain low-resolution information, solid-state NMR spectroscopy is one of the most powerful means for determining the structure and dynamics of membrane bound biomolecules such as antibacterial biomolecules and amyloidogenic proteins; unlike X-ray crystallography and solution NMR spectroscopy, applications of solid-state NMR spectroscopy are not limited by non-crystalline, non-soluble nature or molecular size of membrane-associated biomolecules. This review article focuses on the applications of solid-state NMR techniques to study a few selected antibacterial and amyloid peptides. Solid-state NMR studies revealing the membrane inserted bent α-helical structure associated with the hemolytic activity of bee venom melittin and the chemical shift oscillation analysis used to determine the transmembrane structure (with α-helix and 3 10 -helix in the N- and C-termini, respectively) of antibiotic peptide alamethicin are discussed in detail. Oligomerization of an amyloidogenic islet amyloid polypeptide (IAPP, or also known as amylin) resulting from its aggregation in a membrane environment, molecular interactions of the antifungal natural product amphotericin B with ergosterol in lipid bilayers, and the mechanism of lipid raft formation by sphingomyelin studied using solid state NMR methods are also discussed in this review article. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Dynamic Analysis of Helical Planetary Gear Sets under Combined Force and Moment Loading

    Directory of Open Access Journals (Sweden)

    Yanfang Liu

    2017-01-01

    Full Text Available The dynamic behavior of a single-stage planetary gear set with helical gears of multishaft automotive automatic transmissions has been studied, in which one component of the planetary gear set is imposed by additional external vertical and axial loading from countershaft gear pair in addition to the moment. Under these combined loading conditions, the contributions of the deflections of the ring gear and the carrier cannot be neglected. A three-dimensional nonlinear time-variant dynamic model considering not only the transverse, torsional, axial, and rotational motions of the gears but also the elasticity of the mounted shafts has been developed by combining the lumped parameter method with finite element method. The natural modes and the forced vibration responses due to static transmission errors have been obtained. The proposed dynamic model is employed to describe the effects of the combined external loading condition and positioning on the dynamic behavior of a four-planet system.

  1. Measurement of the dynamic behavior of thin poly(N-isopropylacrylamide) hydrogels and their phase transition temperatures measured using reflectometric interference spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Okada, Fuminori [Konica Minolta, INC. (Japan); Akiyama, Yoshikatsu, E-mail: akiyama.yoshikatsu@twmu.ac.jp, E-mail: akiyama.yoshikatsu@abmes.twmu.ac.jp; Kobayashi, Jun [Tokyo Women’s Medical University (TWIns), Institute of Advanced Biomedical Engineering and Science (Japan); Ninomiya, Hidetaka [Konica Minolta, INC. (Japan); Kanazawa, Hideko [Keio University, Faculty of Pharmacy (Japan); Yamato, Masayuki; Okano, Teruo [Tokyo Women’s Medical University (TWIns), Institute of Advanced Biomedical Engineering and Science (Japan)

    2015-03-15

    Temperature-responsive cell culture surfaces prepared by modifying tissue-culture polystyrene with nanoscale poly(N-isopropylacrylamide) (PIPAAm) hydrogels are widely used as intelligent surfaces for the fabrication of various cell sheets that change with temperature. In this work, the characteristics of nanoscale PIPAAm hydrogels were phenomenologically elucidated on the basis of time-dependent surface evaluations under conditions of changing temperature. Because the dynamic characteristics of the nanoscale hydrogel did not exhibit good performance, the nanoscale PIPAAm hydrogel was analyzed by monitoring its temperature-dependent dynamic swelling/deswelling changes using reflectometric interference spectroscopy (RIfS) on an instrument equipped with a microfluidic system. RIfS measurements under ambient atmosphere provided the precise physical thickness of the dry PIPAAm hydrogel (6.7 nm), which agreed with the atomic force microscopy results (6.6 nm). Simulations of the reflectance spectra revealed that changes in the wavelength of the minimum reflectance (Δλ) were attributable to the changes in the refractive index of the thin PIPAAm hydrogel induced by a temperature-dependent volume phase transition. The temperature-dependent Δλ change was used to monitor the swelling/deswelling behavior of the nanoscale PIPAAm hydrogel. In addition, the phase transition temperature of the thin PIPAAm hydrogel under aqueous conditions was also determined to be the inflection point of the plot of the change in Δλ as a function of temperature. The dynamic behavior of a thin PIPAAm hydrogel chemically deposited on a surface was readily analyzed using a new analytical system with RIfS and microfluidic devices.

  2. Prediction of dynamic cutting force and regenerative chatter stability in inserted cutters milling

    Science.gov (United States)

    Li, Zhongqun; Liu, Qiang; Yuan, Songmei; Huang, Kaisheng

    2013-05-01

    Currently, the modeling of cutting process mainly focuses on two aspects: one is the setup of the universal cutting force model that can be adapted to a broader cutting condition; the other is the setup of the exact cutting force model that can accurately reflect a true cutting process. However, there is little research on the prediction of chatter stablity in milling. Based on the generalized mathematical model of inserted cutters introduced by ENGIN, an improved geometrical, mechanical and dynamic model for the vast variety of inserted cutters widely used in engineering applications is presented, in which the average directional cutting force coefficients are obtained by means of a numerical approach, thus leading to an analytical determination of stability lobes diagram (SLD) on the axial depth of cut. A new kind of SLD on the radial depth of cut is also created to satisfy the special requirement of inserted cutter milling. The corresponding algorithms used for predicting cutting forces, vibrations, dimensional surface finish and stability lobes in inserted cutter milling under different cutting conditions are put forward. Thereafter, a dynamic simulation module of inserted cutter milling is implemented by using hybrid program of Matlab with Visual Basic. Verification tests are conducted on a vertical machine center for Aluminum alloy LC4 by using two different types of inserted cutters, and the effectiveness of the model and the algorithm is verified by the good agreement of simulation result with that of cutting tests under different cutting conditions. The proposed model can predict the cutting process accurately under a variety of cutting conditions, and a high efficient and chatter-free milling operation can be achieved by a cutting condition optimization in industry applications.

  3. Gaining insight into the physics of dynamic atomic force microscopy in complex environments using the VEDA simulator

    Science.gov (United States)

    Kiracofe, Daniel; Melcher, John; Raman, Arvind

    2012-01-01

    Dynamic atomic force microscopy (dAFM) continues to grow in popularity among scientists in many different fields, and research on new methods and operating modes continues to expand the resolution, capabilities, and types of samples that can be studied. But many promising increases in capability are accompanied by increases in complexity. Indeed, interpreting modern dAFM data can be challenging, especially on complicated material systems, or in liquid environments where the behavior is often contrary to what is known in air or vacuum environments. Mathematical simulations have proven to be an effective tool in providing physical insight into these non-intuitive systems. In this article we describe recent developments in the VEDA (virtual environment for dynamic AFM) simulator, which is a suite of freely available, open-source simulation tools that are delivered through the cloud computing cyber-infrastructure of nanoHUB (www.nanohub.org). Here we describe three major developments. First, simulations in liquid environments are improved by enhancements in the modeling of cantilever dynamics, excitation methods, and solvation shell forces. Second, VEDA is now able to simulate many new advanced modes of operation (bimodal, phase-modulation, frequency-modulation, etc.). Finally, nineteen different tip-sample models are available to simulate the surface physics of a wide variety different material systems including capillary, specific adhesion, van der Waals, electrostatic, viscoelasticity, and hydration forces. These features are demonstrated through example simulations and validated against experimental data, in order to provide insight into practical problems in dynamic AFM.

  4. Photodissociation and charge transfer dynamics of negative ions studied with femtosecond photoelectron spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Zanni, Martin Thomas [Univ. of California, Berkeley, CA (United States)

    1999-12-01

    This dissertation presents studies aimed at understanding the potential energy surfaces and dynamics of isolated negative ions, and the effects of solvent on each. Although negative ions play important roles in atmospheric and solution phase chemistry, to a large extent the ground and excited state potential energy surfaces of gas phase negative ions are poorly characterized, and solvent effects even less well understood. In an effort to fill this gap, the author's coworkers and the author have developed a new technique, anion femtosecond photoelectron spectroscopy, and applied it to gas phase photodissociation and charge transfer processes. Studies are presented that (1) characterize the ground and excited states of isolated and clustered anions, (2) monitor the photodissociation dynamics of isolated and clustered anions, and (3) explore the charge-transfer-to-solvent states of atomic iodide clustered with polar and non-polar solvents.

  5. Photodissociation and charge transfer dynamics of negative ions studied with femtosecond photoelectron spectroscopy

    International Nuclear Information System (INIS)

    Zanni, Martin T.

    1999-01-01

    This dissertation presents studies aimed at understanding the potential energy surfaces and dynamics of isolated negative ions, and the effects of solvent on each. Although negative ions play important roles in atmospheric and solution phase chemistry, to a large extent the ground and excited state potential energy surfaces of gas phase negative ions are poorly characterized, and solvent effects even less well understood. In an effort to fill this gap, the author's coworkers and the author have developed a new technique, anion femtosecond photoelectron spectroscopy, and applied it to gas phase photodissociation and charge transfer processes. Studies are presented that (1) characterize the ground and excited states of isolated and clustered anions, (2) monitor the photodissociation dynamics of isolated and clustered anions, and (3) explore the charge-transfer-to-solvent states of atomic iodide clustered with polar and non-polar solvents

  6. Characterization of gold nanoparticle films: Rutherford backscattering spectroscopy, scanning electron microscopy with image analysis, and atomic force microscopy

    Directory of Open Access Journals (Sweden)

    Pia C. Lansåker

    2014-10-01

    Full Text Available Gold nanoparticle films are of interest in several branches of science and technology, and accurate sample characterization is needed but technically demanding. We prepared such films by DC magnetron sputtering and recorded their mass thickness by Rutherford backscattering spectroscopy. The geometric thickness dg—from the substrate to the tops of the nanoparticles—was obtained by scanning electron microscopy (SEM combined with image analysis as well as by atomic force microscopy (AFM. The various techniques yielded an internally consistent characterization of the films. In particular, very similar results for dg were obtained by SEM with image analysis and by AFM.

  7. Structure and Dynamics of Urea/Water Mixtures Investigated by Vibrational Spectroscopy and Molecular Dynamics Simulation

    Science.gov (United States)

    Carr, J. K.; Buchanan, L. E.; Schmidt, J. R.; Zanni, M. T.; Skinner, J. L.

    2013-01-01

    Urea/water is an archetypical “biological” mixture, and is especially well known for its relevance to protein thermodynamics, as urea acts as a protein denaturant at high concentration. This behavior has given rise to an extended debate concerning urea’s influence on water structure. Based on a variety of methods and of definitions of water structure, urea has been variously described as a structure-breaker, a structure-maker, or as remarkably neutral towards water. Because of its sensitivity to microscopic structure and dynamics, vibrational spectroscopy can help resolve these debates. We report experimental and theoretical spectroscopic results for the OD stretch of HOD/H2O/urea mixtures (linear IR, 2DIR, and pump-probe anisotropy decay) and for the CO stretch of urea-D4/D2O mixtures (linear IR only). Theoretical results are obtained using existing approaches for water, and a modification of a frequency map developed for acetamide. All absorption spectra are remarkably insensitive to urea concentration, consistent with the idea that urea only very weakly perturbs water structure. Both this work and experiments by Rezus and Bakker, however, show that water’s rotational dynamics are slowed down by urea. Analysis of the simulations casts doubt on the suggestion that urea immobilizes particular doubly hydrogen bonded water molecules. PMID:23841646

  8. Coherence and population dynamics of chlorophyll excitations in FCP complex: Two-dimensional spectroscopy study

    Energy Technology Data Exchange (ETDEWEB)

    Butkus, Vytautas; Gelzinis, Andrius; Valkunas, Leonas [Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio Ave. 9-III, 10222 Vilnius (Lithuania); Center for Physical Sciences and Technology, Savanoriu Ave. 231, 02300 Vilnius (Lithuania); Augulis, Ramūnas [Center for Physical Sciences and Technology, Savanoriu Ave. 231, 02300 Vilnius (Lithuania); Gall, Andrew; Robert, Bruno [Institut de Biologie et Technologies de Saclay, Bât 532, Commissariat à l’Energie Atomique Saclay, 91191 Gif sur Yvette (France); Büchel, Claudia [Institut für Molekulare Biowissenschaften, Universität Frankfurt, Max-von-Laue-Straße 9, Frankfurt (Germany); Zigmantas, Donatas [Department of Chemical Physics, Lund University, P.O. Box 124, 22100 Lund (Sweden); Abramavicius, Darius, E-mail: darius.abramavicius@ff.vu.lt [Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio Ave. 9-III, 10222 Vilnius (Lithuania)

    2015-06-07

    Energy transfer processes and coherent phenomena in the fucoxanthin–chlorophyll protein complex, which is responsible for the light harvesting function in marine algae diatoms, were investigated at 77 K by using two-dimensional electronic spectroscopy. Experiments performed on femtosecond and picosecond timescales led to separation of spectral dynamics, witnessing evolutions of coherence and population states of the system in the spectral region of Q{sub y} transitions of chlorophylls a and c. Analysis of the coherence dynamics allowed us to identify chlorophyll (Chl) a and fucoxanthin intramolecular vibrations dominating over the first few picoseconds. Closer inspection of the spectral region of the Q{sub y} transition of Chl c revealed previously not identified, mutually non-interacting chlorophyll c states participating in femtosecond or picosecond energy transfer to the Chl a molecules. Consideration of separated coherent and incoherent dynamics allowed us to hypothesize the vibrations-assisted coherent energy transfer between Chl c and Chl a and the overall spatial arrangement of chlorophyll molecules.

  9. Pullback-Forward Dynamics for Damped Schrödinger Equations with Time-Dependent Forcing

    Directory of Open Access Journals (Sweden)

    Lianbing She

    2018-01-01

    Full Text Available This paper deals with pullback dynamics for the weakly damped Schrödinger equation with time-dependent forcing. An increasing, bounded, and pullback absorbing set is obtained if the forcing and its time-derivative are backward uniformly integrable. Also, we obtain the forward absorption, which is only used to deduce the backward compact-decay decomposition according to high and low frequencies. Based on a new existence theorem of a backward compact pullback attractor, we show that the nonautonomous Schrödinger equation has a pullback attractor which is compact in the past. The method of energy, high-low frequency decomposition, Sobolev embedding, and interpolation are quite involved in calculating a priori pullback or forward bound.

  10. Determination of aerodynamic damping and force coefficients of filleted twin cables in dry conditions through passive-dynamic wind tunnel tests

    DEFF Research Database (Denmark)

    Mattiello, E.; Eriksen, M. B.; Georgakis, Christos T.

    /FORCE Technology Climatic Wind Tunnel facility. The measured aerodynamic damping of the twin-cable arrangement in dry conditions was compared to the values obtained from full-scale monitoring and from an analytical model using static force coefficients. The comparison revealed broad agreement in the investigated...... Re range, as did the force coefficients obtained from dynamic and static tests....

  11. Ultrafast Transient Absorption Spectroscopy Investigation of Photoinduced Dynamics in Novel Donor-Acceptor Core-Shell Nanostructures for Organic Photovoltaics

    Science.gov (United States)

    Strain, Jacob; Jamhawi, Abdelqader; Abeywickrama, Thulitha M.; Loomis, Wendy; Rathnayake, Hemali; Liu, Jinjun

    2016-06-01

    Novel donor-acceptor nanostructures were synthesized via covalent synthesis and/or UV cross-linking method. Their photoinduced dynamics were investigated with ultrafast transient absorption (TA) spectroscopy. These new nanostructures are made with the strategy in mind to reduce manufacturing steps in the process of fabricating an organic photovoltaic cell. By imitating the heterojunction interface within a fixed particle domain, several fabrication steps can be bypassed reducing cost and giving more applicability to other film deposition methods. Such applications include aerosol deposition and ink-jet printing. The systems that were studied by TA spectroscopy include PDIB core, PDIB-P3HT core-shell, and PDIB-PANT core-shell which range in size from 60 to 130 nm. Within the experimentally accessible spectra range there resides a region of ground state bleaching, stimulated emission, and excited-state absorption of both neutrals and anions. Control experiments have been carried out to assign these features. At high pump fluences the TA spectra of PDIB core alone also indicate an intramolecular charge separation. The TA spectroscopy results thus far suggest that the core-shells resemble the photoinduced dynamics of a standard film although the particles are dispersed in solution, which indicates the desired outcome of the work.

  12. Features of static and dynamic friction profiles in one and two dimensions on polymer and atomically flat surfaces using atomic force microscopy

    International Nuclear Information System (INIS)

    Watson, G S; Watson, J A

    2008-01-01

    In this paper we correlate the Atomic Force Microscope probe movement with surface location while scanning in the imaging and Force versus distance modes. Static and dynamic stick-slip processes are described on a scale of nanometres to microns on a range of samples. We demonstrate the limits and range of the tip apex being fixed laterally in the force versus distance mode and static friction slope dependence on probe parameters. Micron scale static and dynamic friction can be used to purposefully manipulate soft surfaces to produce well defined frictional gradients

  13. Chemical Force Spectroscopy Evidence Supporting the Layer-by-Layer Model of Organic Matter Binding to Iron (oxy)Hydroxide Mineral Surfaces

    KAUST Repository

    Chassé , Alexander W.; Ohno, Tsutomu; Higgins, Steven R.; Amirbahman, Aria; Yildirim, Nadir; Parr, Thomas B.

    2015-01-01

    © 2015 American Chemical Society. The adsorption of dissolved organic matter (DOM) to metal (oxy)hydroxide mineral surfaces is a critical step for C sequestration in soils. Although equilibrium studies have described some of the factors controlling this process, the molecular-scale description of the adsorption process has been more limited. Chemical force spectroscopy revealed differing adhesion strengths of DOM extracted from three soils and a reference peat soil material to an iron (oxy)hydroxide mineral surface. The DOM was characterized using ultrahigh-resolution negative ion mode electrospray ionization Fourier Transform ion cyclotron resonance mass spectrometry. The results indicate that carboxyl-rich aromatic and N-containing aliphatic molecules of DOM are correlated with high adhesion forces. Increasing molecular mass was shown to decrease the adhesion force between the mineral surface and the DOM. Kendrick mass defect analysis suggests that mechanisms involving two carboxyl groups result in the most stable bond to the mineral surface. We conceptualize these results using a layer-by-layer "onion" model of organic matter stabilization on soil mineral surfaces.

  14. Chemical Force Spectroscopy Evidence Supporting the Layer-by-Layer Model of Organic Matter Binding to Iron (oxy)Hydroxide Mineral Surfaces

    KAUST Repository

    Chassé, Alexander W.

    2015-08-18

    © 2015 American Chemical Society. The adsorption of dissolved organic matter (DOM) to metal (oxy)hydroxide mineral surfaces is a critical step for C sequestration in soils. Although equilibrium studies have described some of the factors controlling this process, the molecular-scale description of the adsorption process has been more limited. Chemical force spectroscopy revealed differing adhesion strengths of DOM extracted from three soils and a reference peat soil material to an iron (oxy)hydroxide mineral surface. The DOM was characterized using ultrahigh-resolution negative ion mode electrospray ionization Fourier Transform ion cyclotron resonance mass spectrometry. The results indicate that carboxyl-rich aromatic and N-containing aliphatic molecules of DOM are correlated with high adhesion forces. Increasing molecular mass was shown to decrease the adhesion force between the mineral surface and the DOM. Kendrick mass defect analysis suggests that mechanisms involving two carboxyl groups result in the most stable bond to the mineral surface. We conceptualize these results using a layer-by-layer "onion" model of organic matter stabilization on soil mineral surfaces.

  15. Investigation of adhesion and mechanical properties of human glioma cells by single cell force spectroscopy and atomic force microscopy.

    Science.gov (United States)

    Andolfi, Laura; Bourkoula, Eugenia; Migliorini, Elisa; Palma, Anita; Pucer, Anja; Skrap, Miran; Scoles, Giacinto; Beltrami, Antonio Paolo; Cesselli, Daniela; Lazzarino, Marco

    2014-01-01

    Active cell migration and invasion is a peculiar feature of glioma that makes this tumor able to rapidly infiltrate into the surrounding brain tissue. In our recent work, we identified a novel class of glioma-associated-stem cells (defined as GASC for high-grade glioma--HG--and Gasc for low-grade glioma--LG) that, although not tumorigenic, act supporting the biological aggressiveness of glioma-initiating stem cells (defined as GSC for HG and Gsc for LG) favoring also their motility. Migrating cancer cells undergo considerable molecular and cellular changes by remodeling their cytoskeleton and cell interactions with surrounding environment. To get a better understanding about the role of the glioma-associated-stem cells in tumor progression, cell deformability and interactions between glioma-initiating stem cells and glioma-associated-stem cells were investigated. Adhesion of HG/LG-cancer cells on HG/LG-glioma-associated stem cells was studied by time-lapse microscopy, while cell deformability and cell-cell adhesion strengths were quantified by indentation measurements by atomic force microscopy and single cell force spectroscopy. Our results demonstrate that for both HG and LG glioma, cancer-initiating-stem cells are softer than glioma-associated-stem cells, in agreement with their neoplastic features. The adhesion strength of GSC on GASC appears to be significantly lower than that observed for Gsc on Gasc. Whereas, GSC spread and firmly adhere on Gasc with an adhesion strength increased as compared to that obtained on GASC. These findings highlight that the grade of glioma-associated-stem cells plays an important role in modulating cancer cell adhesion, which could affect glioma cell migration, invasion and thus cancer aggressiveness. Moreover this work provides evidence about the importance of investigating cell adhesion and elasticity for new developments in disease diagnostics and therapeutics.

  16. Dynamics of Al/Fe{sub 2}O{sub 3} MIC combustion from short single-pulse photothermal initiation and time-resolved spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Stiegman, Albert E.; Park, Chi-Dong; Mileham, Melissa; Van de Burgt, Lambertus J. [Department of Chemistry and Biochemistry, Florida State University Tallahassee, FL (United States); Kramer, Michael P. [AFRL/MNME Eglin AFB, FL (United States)

    2009-08-15

    Time-resolved spectroscopy was used to study the dynamics of the photothermal ignition of Al/Fe{sub 2}O{sub 3} metastable intermolecular composites after single short-pulse laser initiation. The dynamics were recorded in several time domains from nanosecond to microsecond to quantify the dynamics from initial laser excitation to combustion. Time-averaged spectral data were also collected for the overall emission occurring during combustion. (Abstract Copyright [2009], Wiley Periodicals, Inc.)

  17. Lattice dynamics of intercalation and layer compounds by 119Sn Moessbauer effect spectroscopy

    International Nuclear Information System (INIS)

    Herber, R.H.; Davis, R.F.

    1976-01-01

    Gamma ray resonance spectroscopy using the 28-keV radiation from 119 Sn was employed to study the lattice dynamics of layer compounds and their metal atom intercalates. It was found that in solids in which the ( 119 Sn) Moessbauer atom is held either as an ion or as an isolated atom in the structure, both the characteristic lattice temperature (THETA/sub M/) value calculated from the temperature dependence of the recoil-free fraction (evaluated in the high temperature limit where T is greater than THETA/2 and in the absence of significant anharmonic effects) and characteristic temperature (THETA/sub CT/) value calculated by the Craig-Taylor procedure give internally consistent values for the lattice temperature of the solid as probed by the Moessbauer atom. In cases where this probe atom is part of a covalently bonded structure, as for example in the extended polymeric SnS 2 , SnSe 2 and related solids, the difference between THETA/sub M/ and THETA/sub CT/ will be significant, and this difference should be useful in the elucidation of the intermolecular and bonding forces in such solids and their relationship to the solid state properties of these materials. It is noted that the experimental determination of a unique lattice temperature by Moessbauer spectroscopic methods provides the solid state physicist with an additional parameter which should be useful in the characterization of solids, and, more importantly, may serve as a diagnostic tool in the assessment of the effects of systematic changes (such as, for example, compositional variations, radiation damage effects, implantation, and intercalation consequences) brought about in such materials

  18. 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.

  19. 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.

  20. Nonlinear 2D arm dynamics in response to continuous and pulse-shaped force perturbations.

    Science.gov (United States)

    Happee, Riender; de Vlugt, Erwin; van Vliet, Bart

    2015-01-01

    Ample evidence exists regarding the nonlinearity of the neuromuscular system but linear models are widely applied to capture postural dynamics. This study quantifies the nonlinearity of human arm postural dynamics applying 2D continuous force perturbations (0.2-40 Hz) inducing three levels of hand displacement (5, 15, 45 mm RMS) followed by force-pulse perturbations inducing large hand displacements (up to 250 mm) in a position task (PT) and a relax task (RT) recording activity of eight shoulder and elbow muscles. The continuous perturbation data were used to analyze the 2D endpoint dynamics in the frequency domain and to identify reflexive and intrinsic parameters of a linear neuromuscular shoulder-elbow model. Subsequently, it was assessed to what extent the large displacements in response to force pulses could be predicted from the 'small amplitude' linear neuromuscular model. Continuous and pulse perturbation responses with varying amplitudes disclosed highly nonlinear effects. In PT, a larger continuous perturbation induced stiffening with a factor of 1.5 attributed to task adaptation evidenced by increased co-contraction and reflexive activity. This task adaptation was even more profound in the pulse responses where reflexes and displacements were strongly affected by the presence and amplitude of preceding continuous perturbations. In RT, a larger continuous perturbation resulted in yielding with a factor of 3.8 attributed to nonlinear mechanical properties as no significant reflexive activity was found. Pulse perturbations always resulted in yielding where a model fitted to the preceding 5-mm continuous perturbations predicted only 37% of the recorded peak displacements in RT and 79% in PT. This demonstrates that linear neuromuscular models, identified using continuous perturbations with small amplitudes, strongly underestimate displacements in pulse-shaped (e.g., impact) loading conditions. The data will be used to validate neuromuscular models including

  1. Inverse Force Determination on a Small Scale Launch Vehicle Model Using a Dynamic Balance

    Science.gov (United States)

    Ngo, Christina L.; Powell, Jessica M.; Ross, James C.

    2017-01-01

    A launch vehicle can experience large unsteady aerodynamic forces in the transonic regime that, while usually only lasting for tens of seconds during launch, could be devastating if structural components and electronic hardware are not designed to account for them. These aerodynamic loads are difficult to experimentally measure and even harder to computationally estimate. The current method for estimating buffet loads is through the use of a few hundred unsteady pressure transducers and wind tunnel test. Even with a large number of point measurements, the computed integrated load is not an accurate enough representation of the total load caused by buffeting. This paper discusses an attempt at using a dynamic balance to experimentally determine buffet loads on a generic scale hammer head launch vehicle model tested at NASA Ames Research Center's 11' x 11' transonic wind tunnel. To use a dynamic balance, the structural characteristics of the model needed to be identified so that the natural modal response could be and removed from the aerodynamic forces. A finite element model was created on a simplified version of the model to evaluate the natural modes of the balance flexures, assist in model design, and to compare to experimental data. Several modal tests were conducted on the model in two different configurations to check for non-linearity, and to estimate the dynamic characteristics of the model. The experimental results were used in an inverse force determination technique with a psuedo inverse frequency response function. Due to the non linearity, the model not being axisymmetric, and inconsistent data between the two shake tests from different mounting configuration, it was difficult to create a frequency response matrix that satisfied all input and output conditions for wind tunnel configuration to accurately predict unsteady aerodynamic loads.

  2. How to measure load-dependent kinetics of individual motor molecules without a force clamp

    DEFF Research Database (Denmark)

    Sung, J.; Mortensen, Kim; Spudich, J.A.

    2017-01-01

    Single-molecule force spectroscopy techniques, including optical trapping, magnetic trapping, and atomic force microscopy, have provided unprecedented opportunities to understand biological processes at the smallest biological length scales. For example, they have been used to elucidate the molec......Single-molecule force spectroscopy techniques, including optical trapping, magnetic trapping, and atomic force microscopy, have provided unprecedented opportunities to understand biological processes at the smallest biological length scales. For example, they have been used to elucidate...... functions at the single molecule level, such as conformational changes and force-generation of individual motor proteins or force-dependent kinetics in molecular interactions. Here, we describe a new method, “Harmonic Force Spectroscopy (HFS).” With a conventional dual-beam optical trap and a simple...... concepts, experimental setup, step-by-step experimental protocol, theory, data analysis, and results....

  3. Reproducing Quantum Probability Distributions at the Speed of Classical Dynamics: A New Approach for Developing Force-Field Functors.

    Science.gov (United States)

    Sundar, Vikram; Gelbwaser-Klimovsky, David; Aspuru-Guzik, Alán

    2018-04-05

    Modeling nuclear quantum effects is required for accurate molecular dynamics (MD) simulations of molecules. The community has paid special attention to water and other biomolecules that show hydrogen bonding. Standard methods of modeling nuclear quantum effects like Ring Polymer Molecular Dynamics (RPMD) are computationally costlier than running classical trajectories. A force-field functor (FFF) is an alternative method that computes an effective force field that replicates quantum properties of the original force field. In this work, we propose an efficient method of computing FFF using the Wigner-Kirkwood expansion. As a test case, we calculate a range of thermodynamic properties of Neon, obtaining the same level of accuracy as RPMD, but with the shorter runtime of classical simulations. By modifying existing MD programs, the proposed method could be used in the future to increase the efficiency and accuracy of MD simulations involving water and proteins.

  4. Dynamics of Block Copolymer Nanocomposites

    Energy Technology Data Exchange (ETDEWEB)

    Mochrie, Simon G. J.

    2014-09-09

    A detailed study of the dynamics of cadmium sulfide nanoparticles suspended in polystyrene homopolymer matrices was carried out using X-ray photon correlation spectroscopy for temperatures between 120 and 180 °C. For low molecular weight polystyrene homopolymers, the observed dynamics show a crossover from diffusive to hyper-diffusive behavior with decreasing temperatures. For higher molecular weight polystyrene, the nanoparticle dynamics appear hyper-diffusive at all temperatures studied. The relaxation time and characteristic velocity determined from the measured hyper-diffusive dynamics reveal that the activation energy and underlying forces determined are on the order of 2.14 × 10-19 J and 87 pN, respectively. We also carried out a detailed X-ray scattering study of the static and dynamic behavior of a styrene– isoprene diblock copolymer melt with a styrene volume fraction of 0.3468. At 115 and 120 °C, we observe splitting of the principal Bragg peak, which we attribute to phase coexistence of hexagonal cylindrical and cubic double- gyroid structure. In the disordered phase, above 130 °C, we have characterized the dynamics of composition fluctuations via X-ray photon correlation spectroscopy. Near the peak of the static structure factor, these fluctuations show stretched-exponential relaxations, characterized by a stretching exponent of about 0.36 for a range of temperatures immediately above the MST. The corresponding characteristic relaxation times vary exponentially with temperature, changing by a factor of 2 for each 2 °C change in temperature. At low wavevectors, the measured relaxations are diffusive with relaxation times that change by a factor of 2 for each 8 °C change in temperature.

  5. Mapping the dynamical organization of the cell nucleus through fluorescence correlation spectroscopy.

    Science.gov (United States)

    Stortz, Martin; Angiolini, Juan; Mocskos, Esteban; Wolosiuk, Alejandro; Pecci, Adali; Levi, Valeria

    2018-05-01

    The hierarchical organization of the cell nucleus into specialized open reservoirs and the nucleoplasm overcrowding impose restrictions to the mobility of biomolecules and their interactions with nuclear targets. These properties determine that many nuclear functions such as transcription, replication, splicing or DNA repair are regulated by complex, dynamical processes that do not follow simple rules. Advanced fluorescence microscopy tools and, in particular, fluorescence correlation spectroscopy (FCS) provide complementary and exquisite information on the dynamics of fluorescent labeled molecules moving through the nuclear space and are helping us to comprehend the complexity of the nuclear structure. Here, we describe how FCS methods can be applied to reveal the dynamical organization of the nucleus in live cells. Specifically, we provide instructions for the preparation of cellular samples with fluorescent tagged proteins and detail how FCS can be easily instrumented in commercial confocal microscopes. In addition, we describe general rules to set the parameters for one and two-color experiments and the required controls for these experiments. Finally, we review the statistical analysis of the FCS data and summarize the use of numerical simulations as a complementary approach that helps us to understand the complex matrix of molecular interactions network within the nucleus. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Assessment of the dynamics of human glymphatic system by near-infrared spectroscopy.

    Science.gov (United States)

    Myllylä, Teemu; Harju, Markus; Korhonen, Vesa; Bykov, Alexander; Kiviniemi, Vesa; Meglinski, Igor

    2017-08-12

    Fluctuations in brain water content has attracted increasing interest, particularly as regards studies of the glymphatic system, which is connected with the complex organization of dural lymphatic vessels, responsible for cleaning tissue. Disturbances of glymphatic circulation are associated with several brain disorders, including dementia. This article introduces an approach to noninvasive measurement of water dynamics in the human brain utilizing near-infrared spectroscopy (NIRS). We demonstrate the possibility to sense dynamic variations of water content between the skull and grey matter, for instance, in the subarachnoid space. Measured fluctuations in water content, especially in the cerebrospinal fluid (CSF), are assumed to be correlated with the dynamics of glymphatic circulation. The sampling volume for the NIRS optode was estimated by Monte Carlo modelling for the wavelengths of 660, 740, 830 and 980 nm. In addition, using combinations of these wavelengths, this article presents the calculation models for quantifying water and haemodynamics. The presented NIRS technique allows long-term functional brain monitoring, including sleeping time. Furthermore, it is used in combination with different magnetic neuroimaging techniques, particularly magnetic resonance encephalography. Using the combined setup, we report the preliminary results on the interaction between CSF and blood oxygen level-dependent fluctuations. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Three-dimensional scanning force/tunneling spectroscopy at room temperature

    International Nuclear Information System (INIS)

    Sugimoto, Yoshiaki; Ueda, Keiichi; Abe, Masayuki; Morita, Seizo

    2012-01-01

    We simultaneously measured the force and tunneling current in three-dimensional (3D) space on the Si(111)-(7 × 7) surface using scanning force/tunneling microscopy at room temperature. The observables, the frequency shift and the time-averaged tunneling current were converted to the physical quantities of interest, i.e. the interaction force and the instantaneous tunneling current. Using the same tip, the local density of states (LDOS) was mapped on the same surface area at constant height by measuring the time-averaged tunneling current as a function of the bias voltage at every lateral position. LDOS images at negative sample voltages indicate that the tip apex is covered with Si atoms, which is consistent with the Si-Si covalent bonding mechanism for AFM imaging. A measurement technique for 3D force/current mapping and LDOS imaging on the equivalent surface area using the same tip was thus demonstrated. (paper)

  8. Dynamics and rheology under continuous shear flow studied by x-ray photon correlation spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Fluerasu, Andrei [Brookhaven National Laboratory, NSLS-II, Upton, NY 11973 (United States); Kwasniewski, Pawel; Caronna, Chiara; Madsen, Anders [European Synchrotron Radiation Facility, ID10 (Troika), Grenoble 38043 (France); Destremaut, Fanny; Salmon, Jean-Baptiste [LOF, UMR 5258 CNRS-Rhodia Bordeaux 1, 33608 Pessac (France)], E-mail: fluerasu@bnl.gov

    2010-03-15

    X-ray photon correlation spectroscopy (XPCS) has emerged as a unique technique allowing the measurement of dynamics of materials on mesoscopic lengthscales. One of the most common problems associated with the use of bright x-ray beams is beam-induced radiation damage, and this is likely to become an even more limiting factor at future synchrotron and free-electron laser sources. Flowing the sample during data acquisition is one of the simplest methods allowing the radiation damage to be limited. In addition to distributing the dose over many different scatterers, the method also enables new functionalities such as time-resolved studies. Here, we further develop a recently proposed experimental technique that combines XPCS and continuously flowing samples. More specifically, we use a model colloidal suspension to show how the macroscopic advective response to flow and the microscopic dissipative dynamics (diffusion) can be quantified from the x-ray data. Our results show very good quantitative agreement with a Poisseuille-flow hydrodynamical model combined with Brownian mechanics. The method has many potential applications, e.g. in the study of dynamics of glasses and gels under continuous shear/flow, protein aggregation processes and the interplay between dynamics and rheology in complex fluids.

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

    DEFF Research Database (Denmark)

    Li, Xiaozhou; Neumann, Marcus A.; van de Streek, Jacco

    2017-01-01

    of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base...

  10. Preliminary Experimental Results for Indirect Vector-Control of Induction Motor Drives with Forced Dynamics

    Directory of Open Access Journals (Sweden)

    Jan Vittek

    2003-01-01

    Full Text Available The contribution presents an extension of indirect vector control of electric drives employing induction motors to 'Forced Dynamic Control'. This method of control offers an accurate realisation of dynamic response profiles, which can be selected by the user. The developed system can be integrated into a drive with a shaft position encoder or a shaft sensoriess drive, in which only the stator currents are measured. The applied stator voltages are determined by a computed inverter switching algorithm. Simulation results and preliminary experimental results for indirect vector control of an idle running induction motor indicate good agreement with the theoretical predictions.

  11. A feasibility study for experimentally determining dynamic force distribution in a lap joint

    Energy Technology Data Exchange (ETDEWEB)

    Mayes, Randall Lee [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2013-11-01

    Developing constitutive models of the physics in mechanical joints is currently stymied by inability to measure forces and displacements within the joint. The current state of the art estimates whole joint stiffness and energy loss per cycle from external measured force input and one or two acceleration responses. To validate constitutive models beyond this state requires a measurement of the distributed forces and displacements at the joint interface. Unfortunately, introducing measurement devices at the interface completely disrupts the desired physics. A feasibility study is presented for a non-intrusive method of solving for the interface dynamic forces from an inverse problem using full field measured responses. The responses come from the viewable surface of a beam. The noise levels associated with digital image correlation and continuous scanning laser Doppler velocimetry are evaluated from typical beam experiments. Two inverse problems are simulated. One utilizes the extended Sum of Weighted Accelerations Technique (SWAT). The second is a new approach dubbed the method of truncated orthogonal forces. These methods are much more robust if the contact patch geometry is well identified. Various approaches to identifying the contact patch are investigated, including ion marker tracking, Prussian blue and ultrasonic measurements. A typical experiment is conceived for a beam which has a lap joint at one end with a single bolt connecting it to another identical beam. In a virtual test using the beam finite element analysis, it appears that the SWAT inverse method requires evaluation of too many coefficients to adequately identify the force distribution to be viable. However, the method of truncated orthogonal forces appears viable with current digital image correlation (and probably other) imaging techniques.

  12. Momentum distribution, vibrational dynamics, and the potential of mean force in ice

    Science.gov (United States)

    Lin, Lin; Morrone, Joseph A.; Car, Roberto; Parrinello, Michele

    2011-06-01

    By analyzing the momentum distribution obtained from path integral and phonon calculations we find that the protons in hexagonal ice experience an anisotropic quasiharmonic effective potential with three distinct principal frequencies that reflect molecular orientation. Due to the importance of anisotropy, anharmonic features of the environment cannot be extracted from existing experimental distributions that involve the spherical average. The full directional distribution is required, and we give a theoretical prediction for this quantity that could be verified in future experiments. Within the quasiharmonic context, anharmonicity in the ground-state dynamics of the proton is substantial and has quantal origin, a finding that impacts the interpretation of several spectroscopies.

  13. Force Relations and Dynamics of Cutting Knife in a Vertical Disc Mobile Wood Chipper

    Directory of Open Access Journals (Sweden)

    Segun R. BELLO

    2011-06-01

    Full Text Available The force relations and dynamics of cutting knife in a vertical disc wood chipper were investigated. The tool geometry determined include: rake angle (20 deg C; Shear angle, (fi= 52.15 deg C; the mean frictional angle, (t = 5.71 deg C. The analysis and comparison of the cutting forces has shown that the chips separated from the wood are being formed by off cutting, since normal applied force N is compressive in nature, the magnitude of the forces used by the knife on the wood is expected to increase as the cutting edge of the knife goes deeper into the wood until the value of the resisting force acting against the cut wood Ff is reached and exceeded. The evaluated forces acting on the knife and the chip are: F = 3.63Nmm^-1; N = 34.7 Nmm^-1; Fs= 27.45Nmm^-1; Fn =31.92 Nmm^-1; Ft = -8.46Nmm^-1; Fc = 33.85Nmm^-1. The resultant force acting on the tool face, Pr = 34.89Nmm^-1. The specific cutting pressure, Pc and cutting force needed to cut the timber, Fc, are 1.79 × 10^6 N/m2 and 644.84N respectively. The energy consumed in removing a unit volume of material is 69.96kJ/mm^-3 and the maximum power developed in cutting the chip is 3591.77W (4.82hp. The chipper efficiency (86.6% was evaluated by the highest percentage of accepted chip sizes.

  14. Dynamic of cold-atom tips in anharmonic potentials

    Science.gov (United States)

    Menold, Tobias; Federsel, Peter; Rogulj, Carola; Hölscher, Hendrik; Fortágh, József

    2016-01-01

    Background: Understanding the dynamics of ultracold quantum gases in an anharmonic potential is essential for applications in the new field of cold-atom scanning probe microscopy. Therein, cold atomic ensembles are used as sensitive probe tips to investigate nanostructured surfaces and surface-near potentials, which typically cause anharmonic tip motion. Results: Besides a theoretical description of this anharmonic tip motion, we introduce a novel method for detecting the cold-atom tip dynamics in situ and real time. In agreement with theory, the first measurements show that particle interactions and anharmonic motion have a significant impact on the tip dynamics. Conclusion: Our findings will be crucial for the realization of high-sensitivity force spectroscopy with cold-atom tips and could possibly allow for the development of advanced spectroscopic techniques such as Q-control. PMID:28144505

  15. 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

  16. An Optimization-Based Impedance Approach for Robot Force Regulation with Prescribed Force Limits

    Directory of Open Access Journals (Sweden)

    R. de J. Portillo-Vélez

    2015-01-01

    Full Text Available An optimization based approach for the regulation of excessive or insufficient forces at the end-effector level is introduced. The objective is to minimize the interaction force error at the robot end effector, while constraining undesired interaction forces. To that end, a dynamic optimization problem (DOP is formulated considering a dynamic robot impedance model. Penalty functions are considered in the DOP to handle the constraints on the interaction force. The optimization problem is online solved through the gradient flow approach. Convergence properties are presented and the stability is drawn when the force limits are considered in the analysis. The effectiveness of our proposal is validated via experimental results for a robotic grasping task.

  17. Structural analysis of molten Na2O-NaF-SiO2 system by Raman spectroscopy and molecular dynamics simulation

    International Nuclear Information System (INIS)

    Sasaki, Yasushi; Urata, Hidehiro; Ishii, Kuniyoshi

    2003-01-01

    To determine the effect of F ions on the structure of the molten alkali silicate systems, quenched Na 2 O-SiO 2 -NaF systems were investigated by Raman spectroscopy and molecular dynamics simulation. The systematic increase of 1100cm -1 band intensity in the Raman spectra of the silicate melts accompanying the replacement of O by F provides the evidence for concomitant polymerization of melts. From the molecular dynamics simulation, it was confirmed that most of substituted F was mainly coordinated to Na + ions but not Si 4+ ions at least up to 12.5 mol% of F ion content. A small amount of F was found to be coordinated to Si as a non-bridging ion from the molecular dynamics simulation, although there was no recognizable evidence from Raman Spectroscopy. These results were consistent with the mechanism in which F associated with otherwise network-modifying Na rather than with network-forming Si. Since F was associated to Na + ions, the replace of O ion by two F ions promote the polymerization of silicate melts. (author)

  18. Trimethylamine-N-oxide: its hydration structure, surface activity, and biological function, viewed by vibrational spectroscopy and molecular dynamics simulations.

    Science.gov (United States)

    Ohto, Tatsuhiko; Hunger, Johannes; Backus, Ellen H G; Mizukami, Wataru; Bonn, Mischa; Nagata, Yuki

    2017-03-08

    The osmolyte molecule trimethylamine-N-oxide (TMAO) stabilizes the structure of proteins. As functional proteins are generally found in aqueous solutions, an important aspect of this stabilization is the interaction of TMAO with water. Here, we review, using vibrational spectroscopy and molecular dynamics simulations, recent studies on the structure and dynamics of TMAO with its surrounding water molecules. This article ends with an outlook on the open questions on TMAO-protein and TMAO-urea interactions in aqueous environments.

  19. Single-Molecule Force Spectroscopy Trajectories of a Single Protein and Its Polyproteins Are Equivalent: A Direct Experimental Validation Based on A Small Protein NuG2.

    Science.gov (United States)

    Lei, Hai; He, Chengzhi; Hu, Chunguang; Li, Jinliang; Hu, Xiaodong; Hu, Xiaotang; Li, Hongbin

    2017-05-22

    Single-molecule force spectroscopy (SMFS) has become a powerful tool in investigating the mechanical unfolding/folding of proteins at the single-molecule level. Polyproteins made of tandem identical repeats have been widely used in atomic force microscopy (AFM)-based SMFS studies, where polyproteins not only serve as fingerprints to identify single-molecule stretching events, but may also improve statistics of data collection. However, the inherent assumption of such experiments is that all the domains in the polyprotein are equivalent and one SMFS trajectory of stretching a polyprotein made of n domains is equivalent to n trajectories of stretching a single domain. Such an assumption has not been validated experimentally. Using a small protein NuG2 and its polyprotein (NuG2) 4 as model systems, here we use optical trapping (OT) to directly validate this assumption. Our results show that OT experiments on NuG2 and (NuG2) 4 lead to identical parameters describing the unfolding and folding kinetics of NuG2, demonstrating that indeed stretching a polyprotein of NuG2 is equivalent to stretching single NuG2 in force spectroscopy experiments and thus validating the use of polyproteins in SMFS experiments. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Proceedings of the Third Symposium Optical Spectroscopy SOS-84

    International Nuclear Information System (INIS)

    Fassler, D.; Feller, K.H.; Wilhelmi, B.

    1985-01-01

    The main topics of the symposium were: 1) new developments and applications of laser spectroscopy including time resolved UV/VIS spectroscopy, time resolved fluorescence spectroscopy, and laser Raman spectroscopy, 2) dynamics and photokinetics of molecular systems, and 3) spectroscopy and photoprocesses in organized biological systems

  1. Simplistic Coulomb Forces in Molecular Dynamics

    DEFF Research Database (Denmark)

    Hansen, Jesper Schmidt; Schrøder, Thomas; Dyre, J. C.

    2012-01-01

    In this paper we compare the Wolf method to the shifted forces (SF) method for efficient computer simulation of bulk systems with Coulomb forces, taking results from the Ewald summation and particle mesh Ewald methods as representing the true behavior. We find that for the Hansen–McDonald molten...

  2. 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.

  3. Detection of bacterial metabolites through dynamic acquisition from surface enhanced raman spectroscopy substrates integtrated in a centrifugal microfluidic platform

    DEFF Research Database (Denmark)

    Durucan, Onur; Morelli, Lidia; Schmidt, Michael Stenbæk

    2015-01-01

    In this work we present a novel technology that combines the advantages of centrifugal microfluidics with dynamic in-situ Surface Enhanced Raman Spectroscopy (SERS) sensing. Our technology is based on an automated readout system that allows on-line SERS acquisition on a rotating centrifugal...

  4. Ultrafast conductivity dynamics in optically excited InGaN/GaN multiple quantum wells, observed by transient THz spectroscopy

    DEFF Research Database (Denmark)

    Turchinovich, Dmitry; Porte, Henrik; Cooke, David

    2010-01-01

    We investigate ultrafast carrier dynamics in photoexcited InGaN/GaN multiple quantum wells by time-resolved terahertz spectroscopy. The initially very strong built-in piezoelectric field is screened upon photoexcitation by the polarized carriers, and is gradually restored as the carriers recombine...

  5. Static and dynamic stability of the guidance force in a side-suspended HTS maglev system

    Science.gov (United States)

    Zhou, Dajin; Cui, Chenyu; Zhao, Lifeng; Zhang, Yong; Wang, Xiqing; Zhao, Yong

    2017-02-01

    The static and dynamic stability of the guidance force in a side-suspended HTS-PMG (permanent magnetic guideway) system were studied theoretically and experimentally. It is found that there are two types of guidance force that exist in the HTS-PMG system, which are sensitive to the levitation gap and the arrangement of YBCO bulks around the central axis of the PMG. An optimized YBCO array was used to stabilize the system, which enabled a side-suspended HTS-PMG maglev vehicle to run stably at 102 km h-1 on a circular test track with 6.5 m in diameter.

  6. Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, Using Single Molecule Atomic Force Spectroscopy.

    Directory of Open Access Journals (Sweden)

    T Banerjee

    Full Text Available DNA threading intercalators are a unique class of intercalating agents, albeit little biophysical information is available on their intercalative actions. Herein, the intercalative effects of nogalamycin, which is a naturally-occurring DNA threading intercalator, have been investigated by high-resolution atomic force microscopy (AFM and spectroscopy (AFS. The results have been compared with those of the well-known chemotherapeutic drug daunomycin, which is a non-threading classical intercalator bearing structural similarity to nogalamycin. A comparative AFM assessment revealed a greater increase in DNA contour length over the entire incubation period of 48 h for nogalamycin treatment, whereas the contour length increase manifested faster in case of daunomycin. The elastic response of single DNA molecules to an externally applied force was investigated by the single molecule AFS approach. Characteristic mechanical fingerprints in the overstretching behaviour clearly distinguished the nogalamycin/daunomycin-treated dsDNA from untreated dsDNA-the former appearing less elastic than the latter, and the nogalamycin-treated DNA distinguished from the daunomycin-treated DNA-the classically intercalated dsDNA appearing the least elastic. A single molecule AFS-based discrimination of threading intercalation from the classical type is being reported for the first time.

  7. Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, Using Single Molecule Atomic Force Spectroscopy.

    Science.gov (United States)

    Banerjee, T; Banerjee, S; Sett, S; Ghosh, S; Rakshit, T; Mukhopadhyay, R

    2016-01-01

    DNA threading intercalators are a unique class of intercalating agents, albeit little biophysical information is available on their intercalative actions. Herein, the intercalative effects of nogalamycin, which is a naturally-occurring DNA threading intercalator, have been investigated by high-resolution atomic force microscopy (AFM) and spectroscopy (AFS). The results have been compared with those of the well-known chemotherapeutic drug daunomycin, which is a non-threading classical intercalator bearing structural similarity to nogalamycin. A comparative AFM assessment revealed a greater increase in DNA contour length over the entire incubation period of 48 h for nogalamycin treatment, whereas the contour length increase manifested faster in case of daunomycin. The elastic response of single DNA molecules to an externally applied force was investigated by the single molecule AFS approach. Characteristic mechanical fingerprints in the overstretching behaviour clearly distinguished the nogalamycin/daunomycin-treated dsDNA from untreated dsDNA-the former appearing less elastic than the latter, and the nogalamycin-treated DNA distinguished from the daunomycin-treated DNA-the classically intercalated dsDNA appearing the least elastic. A single molecule AFS-based discrimination of threading intercalation from the classical type is being reported for the first time.

  8. Infrared and Raman Spectroscopy of Liquid Water through "First-Principles" Many-Body Molecular Dynamics.

    Science.gov (United States)

    Medders, Gregory R; Paesani, Francesco

    2015-03-10

    Vibrational spectroscopy is a powerful technique to probe the structure and dynamics of water. However, deriving an unambiguous molecular-level interpretation of the experimental spectral features remains a challenge due to the complexity of the underlying hydrogen-bonding network. In this contribution, we present an integrated theoretical and computational framework (named many-body molecular dynamics or MB-MD) that, by systematically removing uncertainties associated with existing approaches, enables a rigorous modeling of vibrational spectra of water from quantum dynamical simulations. Specifically, we extend approaches used to model the many-body expansion of interaction energies to develop many-body representations of the dipole moment and polarizability of water. The combination of these "first-principles" representations with centroid molecular dynamics simulations enables the simulation of infrared and Raman spectra of liquid water under ambient conditions that, without relying on any ad hoc parameters, are in good agreement with the corresponding experimental results. Importantly, since the many-body energy, dipole, and polarizability surfaces employed in the simulations are derived independently from accurate fits to correlated electronic structure data, MB-MD allows for a systematic analysis of the calculated spectra in terms of both electronic and dynamical contributions. The present analysis suggests that, while MB-MD correctly reproduces both the shifts and the shapes of the main spectroscopic features, an improved description of quantum dynamical effects possibly combined with a dissociable water potential may be necessary for a quantitative representation of the OH stretch band.

  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. Force regulated dynamics of RPA on a DNA fork.

    Science.gov (United States)

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

    2016-07-08

    Replication protein A (RPA) is a single-stranded DNA binding protein, involved in most aspects of eukaryotic DNA metabolism. Here, we study the behavior of RPA on a DNA substrate that mimics a replication fork. Using magnetic tweezers we show that both yeast and human RPA can open forked DNA when sufficient external tension is applied. In contrast, at low force, RPA becomes rapidly displaced by the rehybridization of the DNA fork. This process appears to be governed by the binding or the release of an RPA microdomain (toehold) of only few base-pairs length. This gives rise to an extremely rapid exchange dynamics of RPA at the fork. Fork rezipping rates reach up to hundreds of base-pairs per second, being orders of magnitude faster than RPA dissociation from ssDNA alone. Additionally, we show that RPA undergoes diffusive motion on ssDNA, such that it can be pushed over long distances by a rezipping fork. Generally the behavior of both human and yeast RPA homologs is very similar. However, in contrast to yeast RPA, the dissociation of human RPA from ssDNA is greatly reduced at low Mg(2+) concentrations, such that human RPA can melt DNA in absence of force. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Moessbauer spectroscopy-nuclear hyperfine technique for studying dynamic chemical states of iron complexes

    International Nuclear Information System (INIS)

    Maeda, Y.

    2005-01-01

    A brief introduction of Moessbauer spectroscopy will be presented, followed by a discussion of the Moessbauer parameters, isomer shifts, quadrupole splittings, and spectral shapes of complexes in the presence of relaxation of the electronic states of the iron atoms. The usefulness of Moessbauer spectroscopy to demonstrate the dynamic phenomena of electronic states will be discussed in this lecture. (1) The Moessbauer spectra of mixed valence dinuclear and trinuclear iron complexes will be discussed in connection with the chemical structure of the complexes: The values of the quadrupole splittings and isomer shifts of [Fe II Fe III (bpmp) (ppa) 2 ](BF 4 ) 2 increase on raising the temperature, where Hbpmp represents 2,6-bis[bis(2- pyridylmethyl)aminoethyl]-4-methylphenol and ppa is 3-n-phenylpropionic acid. The spectra can be accounted for by postulating intramolecular electron exchange between two energetically inequivalent vibronic states Fe A 2+ Fe B 3+ and Fe A 3+ Fe B 2+ : The apparent time averaged valence states of the iron atoms are 2.2 and 2.8 on the Moessbauer time scale at 293 K. (2) The Moessbauer spectra of iron(III) spin-crossover complexes will be discussed in connection with the spin-transition rate and chemical structure of the complexes. The Moessbauer spectra of spin-crossover iron(III) complexes with LIESST (Light Induced Electronic Spin-State Transition) and of metallomesogens will be discussed to illustrate the extension of this research area by the use of Moessbauer spectroscopy.

  13. Time-resolved vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tokmakoff, Andrei [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Champion, Paul [Northeastern Univ., Boston, MA (United States); Heilweil, Edwin J. [National Inst. of Standards and Technology (NIST), Boulder, CO (United States); Nelson, Keith A. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Ziegler, Larry [Boston Univ., MA (United States)

    2009-05-14

    This document contains the Proceedings from the 14th International Conference on Time-Resolved Vibrational Spectroscopy, which was held in Meredith, NH from May 9-14, 2009. The study of molecular dynamics in chemical reaction and biological processes using time-resolved spectroscopy plays an important role in our understanding of energy conversion, storage, and utilization problems. Fundamental studies of chemical reactivity, molecular rearrangements, and charge transport are broadly supported by the DOE's Office of Science because of their role in the development of alternative energy sources, the understanding of biological energy conversion processes, the efficient utilization of existing energy resources, and the mitigation of reactive intermediates in radiation chemistry. In addition, time-resolved spectroscopy is central to all fiveof DOE's grand challenges for fundamental energy science. The Time-Resolved Vibrational Spectroscopy conference is organized biennially to bring the leaders in this field from around the globe together with young scientists to discuss the most recent scientific and technological advances. The latest technology in ultrafast infrared, Raman, and terahertz spectroscopy and the scientific advances that these methods enable were covered. Particular emphasis was placed on new experimental methods used to probe molecular dynamics in liquids, solids, interfaces, nanostructured materials, and biomolecules.

  14. Polynya dynamics and associated atmospheric forcing at the Ronne Ice Shelf

    Science.gov (United States)

    Ebner, Lars; Heinemann, Günther

    2014-05-01

    The Ronne Ice Shelf is known as one of the most active regions of polynya developments around the Antarctic continent. Low temperatures are prevailing throughout the whole year, particularly in winter. It is generally recognized that polynya formations are primarily forced by offshore winds and secondarily by ocean currents. Many authors have addressed this issue previously at the Ross Ice Shelf and Adélie Coast and connected polynya dynamics to strong katabatic surge events. Such investigations of atmospheric dynamics and simultaneous polynya occurrence are still severely underrepresented for the southwestern part of the Weddell Sea and especially for the Ronne Ice Shelf. Due to the very flat terrain gradients of the ice shelf katabatic winds are of minor importance in that area. Other atmospheric processes must therefore play a crucial role for polynya developments at the Ronne Ice Shelf. High-resolution simulations have been carried out for the Weddell Sea region using the non-hydrostatic NWP model COSMO from the German Meteorological Service (DWD). For the austral autumn and winter (March to August) 2008 daily forecast simulations were conducted with the consideration of daily sea-ice coverage deduced from the passive microwave system AMSR-E. These simulations are used to analyze the synoptic and mesoscale atmospheric dynamics of the Weddell Sea region and find linkages to polynya occurrence at the Ronne Ice Shelf. For that reason, the relation between the surface wind speed, the synoptic pressure gradient in the free atmosphere and polynya area is investigated. Seven significant polynya events are identified for the simulation period, three in the autumn and four in the winter season. It can be shown that in almost all cases synoptic cyclones are the primary polynya forcing systems. In most cases the timely interaction of several passing cyclones in the northern and central Weddell Sea leads to maintenance of a strong synoptic pressure gradient above the

  15. Interaction of an anticancer peptide fragment of azurin with p53 and its isolated domains studied by atomic force spectroscopy.

    Science.gov (United States)

    Bizzarri, Anna Rita; Santini, Simona; Coppari, Emilia; Bucciantini, Monica; Di Agostino, Silvia; Yamada, Tohru; Beattie, Craig W; Cannistraro, Salvatore

    2011-01-01

    p28 is a 28-amino acid peptide fragment of the cupredoxin azurin derived from Pseudomonas aeruginosa that preferentially penetrates cancerous cells and arrests their proliferation in vitro and in vivo. Its antitumor activity reportedly arises from post-translational stabilization of the tumor suppressor p53 normally downregulated by the binding of several ubiquitin ligases. This would require p28 to specifically bind to p53 to inhibit specific ligases from initiating proteosome-mediated degradation. In this study, atomic force spectroscopy, a nanotechnological approach, was used to investigate the interaction of p28 with full-length p53 and its isolated domains at the single molecule level. Analysis of the unbinding forces and the dissociation rate constant suggest that p28 forms a stable complex with the DNA-binding domain of p53, inhibiting the binding of ubiquitin ligases other than Mdm2 to reduce proteasomal degradation of p53.

  16. Diffusing-wave spectroscopy in a standard dynamic light scattering setup

    Science.gov (United States)

    Fahimi, Zahra; Aangenendt, Frank J.; Voudouris, Panayiotis; Mattsson, Johan; Wyss, Hans M.

    2017-12-01

    Diffusing-wave spectroscopy (DWS) extends dynamic light scattering measurements to samples with strong multiple scattering. DWS treats the transport of photons through turbid samples as a diffusion process, thereby making it possible to extract the dynamics of scatterers from measured correlation functions. The analysis of DWS data requires knowledge of the path length distribution of photons traveling through the sample. While for flat sample cells this path length distribution can be readily calculated and expressed in analytical form; no such expression is available for cylindrical sample cells. DWS measurements have therefore typically relied on dedicated setups that use flat sample cells. Here we show how DWS measurements, in particular DWS-based microrheology measurements, can be performed in standard dynamic light scattering setups that use cylindrical sample cells. To do so we perform simple random-walk simulations that yield numerical predictions of the path length distribution as a function of both the transport mean free path and the detection angle. This information is used in experiments to extract the mean-square displacement of tracer particles in the material, as well as the corresponding frequency-dependent viscoelastic response. An important advantage of our approach is that by performing measurements at different detection angles, the average path length through the sample can be varied. For measurements performed on a single sample cell, this gives access to a wider range of length and time scales than obtained in a conventional DWS setup. Such angle-dependent measurements also offer an important consistency check, as for all detection angles the DWS analysis should yield the same tracer dynamics, even though the respective path length distributions are very different. We validate our approach by performing measurements both on aqueous suspensions of tracer particles and on solidlike gelatin samples, for which we find our DWS-based microrheology

  17. Matrix Isolation Spectroscopy Applied to Positron Moderatioin in Cryogenic Solids

    Science.gov (United States)

    2011-07-01

    Current Positron Applications • 2-γ decay exploited in Positron Emission Tomography (PET) scanners. • Positrons localize & annihilate preferentially at...Air Force  Eglin Air Force Base AFRL-RW-EG-TP-2011-024 Matrix Isolation Spectroscopy Applied to Positron Moderation in Cryogenic Solids Distribution... Spectroscopy Applied to Positron Moderation in Cryogenic Solids 5a. CONTRACT NUMBER 5b. GRANT NUMBER 62602F 5c. PROGRAM ELEMENT NUMBER 6

  18. Dynamics of shearing force and its correlations with chemical compositions and dry matter digestibility of stylo ( stem

    Directory of Open Access Journals (Sweden)

    Xuejuan Zi

    2017-12-01

    Full Text Available Objective The study explored the dynamics of shearing force and its correlation with chemical compositions and in vitro dry matter digestibility (IVDMD of stylo. Methods The shearing force, diameter, linear density, chemical composition, and IVDMD of different height stylo stem were investigated. Linear regression analysis was done to determine the relationships between the shearing force and cut height, diameter, chemical composition, or IVDMD. Results The results showed that shearing force of stylo stem increased with plant height increasing and the crude protein (CP content and IVDMD decreased but fiber content increased over time, resulting in decreased forage value. In addition, tall stem had greater shearing force than short stem. Moreover, shearing force is positively correlated with stem diameter, linear density and fiber fraction, but negatively correlated with CP content and IVDMD. Conclusion Overall, shearing force is an indicator more direct, easier and faster to measure than chemical composition and digestibility for evaluation of forage nutritive value related to animal performance. Therefore, it can be used to evaluate the nutritive value of stylo.

  19. Non-linear optical studies of adsorbates: Spectroscopy and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Xiangdong.

    1989-08-01

    In the first part of this thesis, we have established a systematic procedure to apply the surface optical second-harmonic generation (SHG) technique to study surface dynamics of adsorbates. In particular, we have developed a novel technique for studies of molecular surface diffusions. In this technique, the laser-induced desorption with two interfering laser beams is used to produce a monolayer grating of adsorbates. The monolayer grating is detected with diffractions of optical SHG. By monitoring the first-order second-harmonic diffraction, we can follow the time evolution of the grating modulation from which we are able to deduce the diffusion constant of the adsorbates on the surface. We have successfully applied this technique to investigate the surface diffusion of CO on Ni(111). The unique advantages of this novel technique will enable us to readily study anisotropy of a surface diffusion with variable grating orientation, and to investigate diffusion processes of a large dynamic range with variable grating spacings. In the second part of this work, we demonstrate that optical infrared-visible sum-frequency generation (SFG) from surfaces can be used as a viable surface vibrational spectroscopic technique. We have successfully recorded the first vibrational spectrum of a monolayer of adsorbates using optical infrared-visible SFG. The qualitative and quantitative correlation of optical SFG with infrared absorption and Raman scattering spectroscopies are examined and experimentally demonstrated. We have further investigated the possibility to use transient infrared-visible SFG to probe vibrational transients and ultrafast relaxations on surfaces. 146 refs.

  20. Non-linear optical studies of adsorbates: Spectroscopy and dynamics

    International Nuclear Information System (INIS)

    Zhu, Xiangdong.

    1989-08-01

    In the first part of this thesis, we have established a systematic procedure to apply the surface optical second-harmonic generation (SHG) technique to study surface dynamics of adsorbates. In particular, we have developed a novel technique for studies of molecular surface diffusions. In this technique, the laser-induced desorption with two interfering laser beams is used to produce a monolayer grating of adsorbates. The monolayer grating is detected with diffractions of optical SHG. By monitoring the first-order second-harmonic diffraction, we can follow the time evolution of the grating modulation from which we are able to deduce the diffusion constant of the adsorbates on the surface. We have successfully applied this technique to investigate the surface diffusion of CO on Ni(111). The unique advantages of this novel technique will enable us to readily study anisotropy of a surface diffusion with variable grating orientation, and to investigate diffusion processes of a large dynamic range with variable grating spacings. In the second part of this work, we demonstrate that optical infrared-visible sum-frequency generation (SFG) from surfaces can be used as a viable surface vibrational spectroscopic technique. We have successfully recorded the first vibrational spectrum of a monolayer of adsorbates using optical infrared-visible SFG. The qualitative and quantitative correlation of optical SFG with infrared absorption and Raman scattering spectroscopies are examined and experimentally demonstrated. We have further investigated the possibility to use transient infrared-visible SFG to probe vibrational transients and ultrafast relaxations on surfaces. 146 refs

  1. Position Control of Linear Synchronous Motor Drives with Exploitation of Forced Dynamics Control Principles

    Directory of Open Access Journals (Sweden)

    Jan Vittek

    2004-01-01

    Full Text Available Closed-loop position control of mechanisms directly driven by linear synchronous motors with permanent magnets is presented. The control strategy is based on forced dynamic control, which is a form of feedback linearisation, yielding a non-liner multivariable control law to obtain a prescribed linear speed dynamics together with the vector control condition of mutal orthogonality between the stator current and magnetic flux vectors (assuming perfect estimates of the plant parameters. Outer position control loop is closed via simple feedback with proportional gain. Simulations of the design control sysstem, including the drive with power electronic switching, predict the intended drive performance.

  2. Spin-motive Force Induced by Domain Wall Dynamics in the Antiferromagnetic Spin Valve

    Science.gov (United States)

    Sugano, Ryoko; Ichimura, Masahiko; Takahashi, Saburo; Maekawa, Sadamichi; Crest Collaboration

    2014-03-01

    In spite of no net magnetization in antiferromagnetic (AF) textures, the local magnetic properties (Neel magnetization) can be manipulated in a similar fashion to ferromagnetic (F) ones. It is expected that, even in AF metals, spin transfer torques (STTs) lead to the domain wall (DW) motion and that the DW motion induces spin-motive force (SMF). In order to study the Neel magnetization dynamics and the resultant SMF, we treat the nano-structured F1/AF/F2 junction. The F1 and F2 leads behave as a spin current injector and a detector, respectively. Each F lead is fixed in the different magnetization direction. Torsions (DW in AF) are introduced reflecting the fixed magnetization of two F leads. We simulated the STT-induced Neel magnetization dynamics with the injecting current from F1 to F2 and evaluate induced SMF. Based on the adiabatic electron dynamics in the AF texture, Langevin simulations are performed at finite temperature. This research was supported by JST, CREST, Japan.

  3. Force generation by titin folding.

    Science.gov (United States)

    Mártonfalvi, Zsolt; Bianco, Pasquale; Naftz, Katalin; Ferenczy, György G; Kellermayer, Miklós

    2017-07-01

    Titin is a giant protein that provides elasticity to muscle. As the sarcomere is stretched, titin extends hierarchically according to the mechanics of its segments. Whether titin's globular domains unfold during this process and how such unfolded domains might contribute to muscle contractility are strongly debated. To explore the force-dependent folding mechanisms, here we manipulated skeletal-muscle titin molecules with high-resolution optical tweezers. In force-clamp mode, after quenching the force (force trace contained rapid fluctuations and a gradual increase of average force, indicating that titin can develop force via dynamic transitions between its structural states en route to the native conformation. In 4 M urea, which destabilizes H-bonds hence the consolidated native domain structure, the net force increase disappeared but the fluctuations persisted. Thus, whereas net force generation is caused by the ensemble folding of the elastically-coupled domains, force fluctuations arise due to a dynamic equilibrium between unfolded and molten-globule states. Monte-Carlo simulations incorporating a compact molten-globule intermediate in the folding landscape recovered all features of our nanomechanics results. The ensemble molten-globule dynamics delivers significant added contractility that may assist sarcomere mechanics, and it may reduce the dissipative energy loss associated with titin unfolding/refolding during muscle contraction/relaxation cycles. © 2017 The Protein Society.

  4. Optimized Free Energies from Bidirectional Single-Molecule Force Spectroscopy

    Science.gov (United States)

    Minh, David D. L.; Adib, Artur B.

    2008-05-01

    An optimized method for estimating path-ensemble averages using data from processes driven in opposite directions is presented. Based on this estimator, bidirectional expressions for reconstructing free energies and potentials of mean force from single-molecule force spectroscopy—valid for biasing potentials of arbitrary stiffness—are developed. Numerical simulations on a model potential indicate that these methods perform better than unidirectional strategies.

  5. Dynamic electro-thermal modeling of all-vanadium redox flow battery with forced cooling strategies

    International Nuclear Information System (INIS)

    Wei, Zhongbao; Zhao, Jiyun; Xiong, Binyu

    2014-01-01

    Highlights: • A dynamic electro-thermal model is proposed for VRB with forced cooling. • The Foster network is adopted to model the battery cooling process. • Both the electrolyte temperature and terminal voltage can be accurately predicted. • The flow rate of electrolyte and coolant significantly impact battery performance. - Abstract: The present study focuses on the dynamic electro-thermal modeling for the all-vanadium redox flow battery (VRB) with forced cooling strategies. The Foster network is adopted to dynamically model the heat dissipation of VRB with heat exchangers. The parameters of Foster network are extracted by fitting the step response of it to the results of linearized CFD model. Then a complete electro-thermal model is proposed by coupling the heat generation model, Foster network and electrical model. Results show that the established model has nearly the same accuracy with the nonlinear CFD model in electrolyte temperature prediction but drastically improves the computational efficiency. The modeled terminal voltage is also benchmarked with the experimental data under different current densities. The electrolyte temperature is found to be significantly influenced by the flow rate of coolant. As compared, although the electrolyte flow rate has unremarkable impact on electrolyte temperature, its effect on system pressure drop and battery efficiency is significant. Increasing the electrolyte flow rate improves the coulombic efficiency, voltage efficiency and energy efficiency simultaneously but at the expense of higher pump power demanded. An optimal flow rate exists for each operating condition to maximize the system efficiency

  6. Crystal spectroscopy of silicon aero-gel end-caps driven by a dynamic hohlraum on Z

    International Nuclear Information System (INIS)

    Nash, T.J.; Sanford, T.W.L.; Mock, R.C.; Leeper, R.J.; Chandler, G.A.; Bailey, J.E.; McKenney, J.L.; Mehlhorn, T.A.; Seaman, J.F.; McGurn, J.; Schroen, D.; Russell, C.; Lake, P.E.; Jobe, D.O.; Gilliland, T.; Nielsen, D.S.; Lucas, J.; Moore, T.; Torres, J.A.; MacFarlane, J.J.; Apruzese, J.P.; Chrien, R.; Idzorek, G.; Peterson, D.L.; Watt, R.

    2005-01-01

    We present results from crystal spectroscopic analysis of silicon aero-gel foams heated by dynamic hohlraums on Z. The dynamic hohlraum on Z creates a radiation source with a 230-eV average temperature over a 2.4-mm diameter. In these experiments silicon aero-gel foams with 10-mg/cm3 densities and 1.7-mm lengths were placed on both ends of the dynamic hohlraum. Several crystal spectrometers were placed both above and below the z-pinch to diagnose the temperature of the silicon aero-gel foam using the K-shell lines of silicon. The crystal spectrometers were (1) temporally integrated and spatially resolved, (2) temporally resolved and spatially integrated, and (3) both temporally and spatially resolved. The results indicate that the dynamic hohlraum heats the silicon aero-gel to approximately 150-eV at peak power. As the dynamic hohlraum source cools after peak power the silicon aero-gel continues to heat and jets axially at an average velocity of approximately 50-cm/μs. The spectroscopy has also shown that the reason for the up/down asymmetry in radiated power on Z is that tungsten enters the line-of-sight on the bottom of the machine much more than on the top

  7. Dynamics of colloidal particles in ice

    KAUST Repository

    Spannuth, Melissa

    2011-01-01

    We use x-ray photon correlation spectroscopy (XPCS) to probe the dynamics of colloidal particles in polycrystalline ice. During freezing, the dendritic ice morphology and rejection of particles from the ice created regions of high particle density, where some of the colloids were forced into contact and formed disordered aggregates. The particles in these high density regions underwent ballistic motion, with a characteristic velocity that increased with temperature. This ballistic motion is coupled with both stretched and compressed exponential decays of the intensity autocorrelation function. We suggest that this behavior could result from ice grain boundary migration. © 2011 American Institute of Physics.

  8. 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)

  9. Atomic force microscope adhesion measurements and atomistic molecular dynamics simulations at different humidities

    International Nuclear Information System (INIS)

    Seppä, Jeremias; Sairanen, Hannu; Korpelainen, Virpi; Husu, Hannu; Heinonen, Martti; Lassila, Antti; Reischl, Bernhard; Raiteri, Paolo; Rohl, Andrew L; Nordlund, Kai

    2017-01-01

    Due to their operation principle atomic force microscopes (AFMs) are sensitive to all factors affecting the detected force between the probe and the sample. Relative humidity is an important and often neglected—both in experiments and simulations—factor in the interaction force between AFM probe and sample in air. This paper describes the humidity control system designed and built for the interferometrically traceable metrology AFM (IT-MAFM) at VTT MIKES. The humidity control is based on circulating the air of the AFM enclosure via dryer and humidifier paths with adjustable flow and mixing ratio of dry and humid air. The design humidity range of the system is 20–60 %rh. Force–distance adhesion studies at humidity levels between 25 %rh and 53 %rh are presented and compared to an atomistic molecular dynamics (MD) simulation. The uncertainty level of the thermal noise method implementation used for force constant calibration of the AFM cantilevers is 10 %, being the dominant component of the interaction force measurement uncertainty. Comparing the simulation and the experiment, the primary uncertainties are related to the nominally 7 nm radius and shape of measurement probe apex, possible wear and contamination, and the atomistic simulation technique details. The interaction forces are of the same order of magnitude in simulation and measurement (5 nN). An elongation of a few nanometres of the water meniscus between probe tip and sample, before its rupture, is seen in simulation upon retraction of the tip in higher humidity. This behaviour is also supported by the presented experimental measurement data but the data is insufficient to conclusively verify the quantitative meniscus elongation. (paper)

  10. From Femtosecond Dynamics to Breast Cancer Diagnosis by Raman Spectroscopy

    International Nuclear Information System (INIS)

    Abramczyk, H.; Placek, I.; Brozek-Pluska, B.; Kurczewski, K.; Morawiec, Z.; Tazbir, M.

    2007-01-01

    This paper presents new results based on Raman spectroscopy and demonstrates its utilisation as a diagnostic and development tool with the key advantage in breast cancer research. Applications of Raman spectroscopy in cancer research are in the early stages of development. However, research presented here as well as performed in a few other laboratories demonstrate the ability of Raman spectroscopy to accurately characterize cancer tissue and distinguish between normal, malignant and benign types. The main goals of bio-Raman spectroscopy at this stage are threefold. Firstly, the aim is to develop the diagnostic ability of Raman spectroscopy so it can be implemented in a clinical environment, producing accurate and rapid diagnoses. Secondly, the aim is to optimize the technique as a diagnostic tool for the non-invasive real time medical applications. Thirdly, the aim is to formulate some hypothesis based on Raman spectroscopy on the molecular mechanism which drives the transformation of normal human cells into highly malignant derivatives. To the best of our knowledge, this is the most statistically reliable report on Raman spectroscopy-based diagnosis of breast cancers among the world women population

  11. Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory.

    Science.gov (United States)

    Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex; Niklasson, Anders M N; Head-Gordon, Teresa; Skylaris, Chris-Kriton

    2017-03-28

    Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities are treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes-in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.

  12. Characterization of Bifunctional Spin Labels for Investigating the Structural and Dynamic Properties of Membrane Proteins Using EPR Spectroscopy.

    Science.gov (United States)

    Sahu, Indra D; Craig, Andrew F; Dunagum, Megan M; McCarrick, Robert M; Lorigan, Gary A

    2017-10-05

    Site-directed spin labeling (SDSL) coupled with electron paramagnetic resonance (EPR) spectroscopy is a very powerful technique to study structural and dynamic properties of membrane proteins. The most widely used spin label is methanthiosulfonate (MTSL). However, the flexibility of this spin label introduces greater uncertainties in EPR measurements obtained for determining structures, side-chain dynamics, and backbone motion of membrane protein systems. Recently, a newer bifunctional spin label (BSL), 3,4-bis(methanethiosulfonylmethyl)-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-1-yloxy, has been introduced to overcome the dynamic limitations associated with the MTSL spin label and has been invaluable in determining protein backbone dynamics and inter-residue distances due to its restricted internal motion and fewer size restrictions. While BSL has been successful in providing more accurate information about the structure and dynamics of several proteins, a detailed characterization of the spin label is still lacking. In this study, we characterized BSLs by performing CW-EPR spectral line shape analysis as a function of temperature on spin-labeled sites inside and outside of the membrane for the integral membrane protein KCNE1 in POPC/POPG lipid bilayers and POPC/POPG lipodisq nanoparticles. The experimental data revealed a powder pattern spectral line shape for all of the KCNE1-BSL samples at 296 K, suggesting the motion of BSLs approaches the rigid limit regime for these series of samples. BSLs were further utilized to report for the first time the distance measurement between two BSLs attached on an integral membrane protein KCNE1 in POPC/POPG lipid bilayers at room temperature using dipolar line broadening CW-EPR spectroscopy. The CW dipolar line broadening EPR data revealed a 15 ± 2 Å distance between doubly attached BSLs on KCNE1 (53/57-63/67) which is consistent with molecular dynamics modeling and the solution NMR structure of KCNE1 which yielded a

  13. Dynamic domains of amyloid fibrils can be site-specifically assigned with proton detected 3D NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Falk, Alexander S.; Siemer, Ansgar B., E-mail: asiemer@usc.edu [Keck School of Medicine of USC, Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute (United States)

    2016-11-15

    Several amyloid fibrils have cores framed by highly dynamic, intrinsically disordered, domains that can play important roles for function and toxicity. To study these domains in detail using solid-state NMR spectroscopy, site-specific resonance assignments are required. Although the rapid dynamics of these domains lead to considerable averaging of orientation-dependent NMR interactions and thereby line-narrowing, the proton linewidths observed in these samples is far larger than what is regularly observed in solution. Here, we show that it is nevertheless possible to record 3D HNCO, HNCA, and HNcoCA spectra on these intrinsically disordered domains and to obtain site-specific assignments.

  14. Dynamic domains of amyloid fibrils can be site-specifically assigned with proton detected 3D NMR spectroscopy

    International Nuclear Information System (INIS)

    Falk, Alexander S.; Siemer, Ansgar B.

    2016-01-01

    Several amyloid fibrils have cores framed by highly dynamic, intrinsically disordered, domains that can play important roles for function and toxicity. To study these domains in detail using solid-state NMR spectroscopy, site-specific resonance assignments are required. Although the rapid dynamics of these domains lead to considerable averaging of orientation-dependent NMR interactions and thereby line-narrowing, the proton linewidths observed in these samples is far larger than what is regularly observed in solution. Here, we show that it is nevertheless possible to record 3D HNCO, HNCA, and HNcoCA spectra on these intrinsically disordered domains and to obtain site-specific assignments.

  15. Development of Swimming Human Simulation Model Considering Rigid Body Dynamics and Unsteady Fluid Force for Whole Body

    Science.gov (United States)

    Nakashima, Motomu; Satou, Ken; Miura, Yasufumi

    The purpose of this study is to develop a swimming human simulation model considering rigid body dynamics and unsteady fluid force for the whole body, which will be utilized to analyze various dynamical problems in human swimming. First, the modeling methods and their formulations for the human body and the fluid force are respectively described. Second, experiments to identify the coefficients of the normal drag and the added mass are conducted by use of an experimental setup, in which a limb model rotates in the water, and its rotating angle and the bending moment at the root are measured. As the result of the identification, the present model for the fluid force was found to have satisfactory performance in order to represent the unsteady fluctuations of the experimental data, although it has 10% error. Third, a simulation for the gliding position is conducted in order to identify the tangential drag coefficient. Finally, a simulation example of standard six beat front crawl swimming is shown. The swimming speed of the simulation became a reasonable value, indicating the validity of the present simulation model, although it is 7.5% lower than the actual swimming.

  16. Intracellular localization and dynamics of Hypericin loaded PLLA nanocarriers by image correlation spectroscopy.

    Science.gov (United States)

    Penjweini, Rozhin; Deville, Sarah; D'Olieslaeger, Lien; Berden, Mandy; Ameloot, Marcel; Ethirajan, Anitha

    2015-11-28

    The study of cell-nanoparticle interactions is an important aspect for understanding drug delivery using nanocarriers. In this regard, advances in fluorescence based microscopy are useful for the investigation of temporal and spatial behavior of nanoparticles (NPs) within the intracellular environment. In this work, we focus on the delivery of the naturally-occurring hydrophobic photosensitizer Hypericin in human lung carcinoma A549 cells by using biodegradable poly L-lactic acid NPs. For the first time, Hypericin containing NPs are prepared by combining the miniemulsion technique with the solvent evaporation method. This approach yields an efficient loading of the NPs with Hypericin and allows for additional cargo molecules. To monitor the release of Hypercin from the NPs, an additional fluorescent lipophilic dye Coumarin-6 is incorporated in the NPs. Temporal and spatiotemporal image correlation spectroscopy is used to determine the fate of the NPs carrying the potential cargo. Both directed and non-directed motions are detected. By using image cross-correlation spectroscopy and specific fluorescent labeling of endosomes, lysosomes and mitochondria, the dynamics of the cargo loaded NPs in association with the organelles is studied. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. A Force-Activated Trip Switch Triggers Rapid Dissociation of a Colicin from Its Immunity Protein

    Science.gov (United States)

    Farrance, Oliver E.; Hann, Eleanore; Kaminska, Renata; Housden, Nicholas G.; Derrington, Sasha R.; Kleanthous, Colin; Radford, Sheena E.; Brockwell, David J.

    2013-01-01

    Colicins are protein antibiotics synthesised by Escherichia coli strains to target and kill related bacteria. To prevent host suicide, colicins are inactivated by binding to immunity proteins. Despite their high avidity (Kd≈fM, lifetime ≈4 days), immunity protein release is a pre-requisite of colicin intoxication, which occurs on a timescale of minutes. Here, by measuring the dynamic force spectrum of the dissociation of the DNase domain of colicin E9 (E9) and immunity protein 9 (Im9) complex using an atomic force microscope we show that application of low forces (force-triggered increase in off-rate a trip bond. Using mutational analysis, we elucidate the mechanism of this switch in affinity. We show that the N-terminal region of E9, which has sparse contacts with the hydrophobic core, is linked to an allosteric activator region in E9 (residues 21–30) whose remodelling triggers immunity protein release. Diversion of the force transduction pathway by the introduction of appropriately positioned disulfide bridges yields a force resistant complex with a lifetime identical to that measured by ensemble techniques. A trip switch within E9 is ideal for its function as it allows bipartite complex affinity, whereby the stable colicin:immunity protein complex required for host protection can be readily converted to a kinetically unstable complex whose dissociation is necessary for cellular invasion and competitor death. More generally, the observation of two force phenotypes for the E9:Im9 complex demonstrates that force can re-sculpt the underlying energy landscape, providing new opportunities to modulate biological reactions in vivo; this rationalises the commonly observed discrepancy between off-rates measured by dynamic force spectroscopy and ensemble methods. PMID:23431269

  18. Ionization and dissociation dynamics of vinyl bromide probed by femtosecond extreme ultraviolet transient absorption spectroscopy

    International Nuclear Information System (INIS)

    Lin, Ming-Fu; Neumark, Daniel M.; Gessner, Oliver; Leone, Stephen R.

    2014-01-01

    Strong-field induced ionization and dissociation dynamics of vinyl bromide, CH 2 =CHBr, are probed using femtosecond extreme ultraviolet (XUV) transient absorption spectroscopy. Strong-field ionization is initiated with an intense femtosecond, near infrared (NIR, 775 nm) laser field. Femtosecond XUV pulses covering the photon energy range of 50-72 eV probe the subsequent dynamics by measuring the time-dependent spectroscopic features associated with transitions of the Br (3d) inner-shell electrons to vacancies in molecular and atomic valence orbitals. Spectral signatures are observed for the depletion of neutral C 2 H 3 Br, the formation of C 2 H 3 Br + ions in their ground (X ~ ) and first excited (A ~ ) states, the production of C 2 H 3 Br ++ ions, and the appearance of neutral Br ( 2 P 3/2 ) atoms by dissociative ionization. The formation of free Br ( 2 P 3/2 ) atoms occurs on a timescale of 330 ± 150 fs. The ionic A ~ state exhibits a time-dependent XUV absorption energy shift of ∼0.4 eV within the time window of the atomic Br formation. The yield of Br atoms correlates with the yield of parent ions in the A ~ state as a function of NIR peak intensity. The observations suggest that a fraction of vibrationally excited C 2 H 3 Br + (A ~ ) ions undergoes intramolecular vibrational energy redistribution followed by the C–Br bond dissociation. The C 2 H 3 Br + (X ~ ) products and the majority of the C 2 H 3 Br ++ ions are relatively stable due to a deeper potential well and a high dissociation barrier, respectively. The results offer powerful new insights about orbital-specific electronic processes in high field ionization, coupled vibrational relaxation and dissociation dynamics, and the correlation of valence hole-state location and dissociation in polyatomic molecules, all probed simultaneously by ultrafast table-top XUV spectroscopy

  19. Chaos as an intermittently forced linear system.

    Science.gov (United States)

    Brunton, Steven L; Brunton, Bingni W; Proctor, Joshua L; Kaiser, Eurika; Kutz, J Nathan

    2017-05-30

    Understanding the interplay of order and disorder in chaos is a central challenge in modern quantitative science. Approximate linear representations of nonlinear dynamics have long been sought, driving considerable interest in Koopman theory. We present a universal, data-driven decomposition of chaos as an intermittently forced linear system. This work combines delay embedding and Koopman theory to decompose chaotic dynamics into a linear model in the leading delay coordinates with forcing by low-energy delay coordinates; this is called the Hankel alternative view of Koopman (HAVOK) analysis. This analysis is applied to the Lorenz system and real-world examples including Earth's magnetic field reversal and measles outbreaks. In each case, forcing statistics are non-Gaussian, with long tails corresponding to rare intermittent forcing that precedes switching and bursting phenomena. The forcing activity demarcates coherent phase space regions where the dynamics are approximately linear from those that are strongly nonlinear.The huge amount of data generated in fields like neuroscience or finance calls for effective strategies that mine data to reveal underlying dynamics. Here Brunton et al.develop a data-driven technique to analyze chaotic systems and predict their dynamics in terms of a forced linear model.

  20. Reduced order dynamic model for polysaccharides molecule attached to an atomic force microscope

    International Nuclear Information System (INIS)

    Tang Deman; Li Aiqin; Attar, Peter; Dowell, Earl H.

    2004-01-01

    A dynamic analysis and numerical simulation has been conducted of a polysaccharides molecular structure (a ten (10) single-α-D-glucose molecule chain) connected to a moving atomic force microscope (AFM). Sinusoidal base excitation of the AFM cantilevered beam is considered. First a linearized perturbation model is constructed for the complex polysaccharides molecular structure. Then reduced order (dynamic) models based upon a proper orthogonal decomposition (POD) technique are constructed using global modes for both the linearized perturbation model and for the full nonlinear model. The agreement between the original and reduced order models (ROM/POD) is very good even when only a few global modes are included in the ROM for either the linear case or for the nonlinear case. The computational advantage of the reduced order model is clear from the results presented

  1. A review of a method for dynamic load distribution, dynamical modeling, and explicit internal force control when two manipulators mutually lift and transport a rigid body object

    International Nuclear Information System (INIS)

    Unseren, M.A.

    1997-01-01

    The paper reviews a method for modeling and controlling two serial link manipulators which mutually lift and transport a rigid body object in a three dimensional workspace. A new vector variable is introduced which parameterizes the internal contact force controlled degrees of freedom. A technique for dynamically distributing the payload between the manipulators is suggested which yields a family of solutions for the contact forces and torques the manipulators impart to the object. A set of rigid body kinematic constraints which restrict the values of the joint velocities of both manipulators is derived. A rigid body dynamical model for the closed chain system is first developed in the joint space. The model is obtained by generalizing the previous methods for deriving the model. The joint velocity and acceleration variables in the model are expressed in terms of independent pseudovariables. The pseudospace model is transformed to obtain reduced order equations of motion and a separate set of equations governing the internal components of the contact forces and torques. A theoretic control architecture is suggested which explicitly decouples the two sets of equations comprising the model. The controller enables the designer to develop independent, non-interacting control laws for the position control and internal force control of the system

  2. A review of a method for dynamic load distribution, dynamical modeling, and explicit internal force control when two manipulators mutually lift and transport a rigid body object

    Energy Technology Data Exchange (ETDEWEB)

    Unseren, M.A.

    1997-04-20

    The paper reviews a method for modeling and controlling two serial link manipulators which mutually lift and transport a rigid body object in a three dimensional workspace. A new vector variable is introduced which parameterizes the internal contact force controlled degrees of freedom. A technique for dynamically distributing the payload between the manipulators is suggested which yields a family of solutions for the contact forces and torques the manipulators impart to the object. A set of rigid body kinematic constraints which restrict the values of the joint velocities of both manipulators is derived. A rigid body dynamical model for the closed chain system is first developed in the joint space. The model is obtained by generalizing the previous methods for deriving the model. The joint velocity and acceleration variables in the model are expressed in terms of independent pseudovariables. The pseudospace model is transformed to obtain reduced order equations of motion and a separate set of equations governing the internal components of the contact forces and torques. A theoretic control architecture is suggested which explicitly decouples the two sets of equations comprising the model. The controller enables the designer to develop independent, non-interacting control laws for the position control and internal force control of the system.

  3. The Reaction Mechanism of Claisen Rearrangement Obtained by Transition State Spectroscopy and Single Direct-Dynamics Trajectory

    Directory of Open Access Journals (Sweden)

    Takayoshi Kobayashi

    2013-02-01

    Full Text Available Chemical bond breaking and formation during chemical reactions can be observed using “transition state spectroscopy”. Comparing the measurement result of the transition state spectroscopy with the simulation result of single direct-dynamics trajectory, we have elucidated the reaction dynamics of Claisen rearrangement of allyl vinyl ether. Observed the reaction of the neat sample liquid, we have estimated the time constants of transformation from straight-chain structure to aromatic-like six-membered ring structure forming the C1-C6 bond. The result clarifies that the reaction proceeds via three steps taking longer time than expected from the gas phase calculation. This finding provides new hypothesis and discussions, helping the development of the field of reaction mechanism analysis.

  4. Development of time-resolved electron momentum spectroscopy. Toward real-time imaging of frontier electrons in molecular reactions

    International Nuclear Information System (INIS)

    Yamazaki, M.; Takahashi, M.

    2016-01-01

    This report will introduce a new experimental technique to readers, which we would like to propose towards advances in the field of molecular reaction dynamics. It is time-resolved electron momentum spectroscopy and aims to take in momentum space snapshots of the rapid change of molecular orbitals, which is the driving force behind any structural changes occurring in transient molecules. Following a description of the working principle of the technique, some preliminary result will be presented in order to illustrate the current performance of the apparatus. (author)

  5. Single-molecule force-conductance spectroscopy of hydrogen-bonded complexes

    DEFF Research Database (Denmark)

    Pirrotta, Alessandro; De Vico, Luca; Solomon, Gemma C.

    2017-01-01

    to inform about molecular recognition events at the single-molecule limit. For this, we consider the force-conductance characteristics of a prototypical class of hydrogen bonded bimolecular complexes sandwiched between gold electrodes. The complexes consist of derivatives of a barbituric acid and a Hamilton...... is mechanically manipulated. The implication is that force and conductance provide complementary information about the evolution of molecules in junctions that can be used to interrogate basic structure-transport relations at the single-molecule limit....

  6. Segment-scale, force-level theory of mesoscopic dynamic localization and entropic elasticity in entangled chain polymer liquids

    Science.gov (United States)

    Dell, Zachary E.; Schweizer, Kenneth S.

    2017-04-01

    We develop a segment-scale, force-based theory for the breakdown of the unentangled Rouse model and subsequent emergence of isotropic mesoscopic localization and entropic elasticity in chain polymer liquids in the absence of ergodicity-restoring anisotropic reptation or activated hopping motion. The theory is formulated in terms of a conformational N-dynamic-order-parameter generalized Langevin equation approach. It is implemented using a universal field-theoretic Gaussian thread model of polymer structure and closed at the level of the chain dynamic second moment matrix. The physical idea is that the isotropic Rouse model fails due to the dynamical emergence, with increasing chain length, of time-persistent intermolecular contacts determined by the combined influence of local uncrossability, long range polymer connectivity, and a self-consistent treatment of chain motion and the dynamic forces that hinder it. For long chain melts, the mesoscopic localization length (identified as the tube diameter) and emergent entropic elasticity predictions are in near quantitative agreement with experiment. Moreover, the onset chain length scales with the semi-dilute crossover concentration with a realistic numerical prefactor. Distinctive novel predictions are made for various off-diagonal correlation functions that quantify the full spatial structure of the dynamically localized polymer conformation. As the local excluded volume constraint and/or intrachain bonding spring are softened to allow chain crossability, the tube diameter is predicted to swell until it reaches the radius-of-gyration at which point mesoscopic localization vanishes in a discontinuous manner. A dynamic phase diagram for such a delocalization transition is constructed, which is qualitatively consistent with simulations and the classical concept of a critical entanglement degree of polymerization.

  7. High-speed dynamic atomic force microscopy by using a Q-controlled cantilever eigenmode as an actuator

    Energy Technology Data Exchange (ETDEWEB)

    Balantekin, M., E-mail: mujdatbalantekin@iyte.edu.tr

    2015-02-15

    We present a high-speed operating method with feedback to be used in dynamic atomic force microscope (AFM) systems. In this method we do not use an actuator that has to be employed to move the tip or the sample as in conventional AFM setups. Instead, we utilize a Q-controlled eigenmode of an AFM cantilever to perform the function of the actuator. Simulations show that even with an ordinary tapping-mode cantilever, imaging speed can be increased by about 2 orders of magnitude compared to conventional dynamic AFM imaging. - Highlights: • A high-speed imaging method is developed for dynamic-AFM systems. • An eigenmode of an AFM cantilever is utilized to perform fast actuation. • Simulations show 2 orders of magnitude increase in scan speed. • The time spent for dynamic-AFM imaging experiments will be minimized.

  8. Laser spectroscopy probes the nucleus

    International Nuclear Information System (INIS)

    Griffith, J.; Billowes, J.

    1998-01-01

    Extremely sensitive optical measurements are shedding new light on the shape and size of nuclei, and the properties of nuclear matter far from stability. Of the 7000 or so isotopes known to nuclear physicists, less than 270 are stable. In general isotopes become more and more unstable as we move away from the so-called valley of stability, and therefore become more difficult to study in experiments. The tests of the theory also become more demanding. Laser spectroscopy is one of the techniques that is helping to explore the properties of these isotopes and improve our understanding of the forces inside the nucleus. High-resolution laser spectroscopy of short-lived radioactive atoms now makes it possible to measure the nuclear charge radius of many elements, including many isotopes far from stability. The method can reveal fine details of the sizes, shapes and structures of nuclei. In addition, laser spectroscopy is making significant contributions to our understanding of the nuclear force in unstable nuclei with unusual, or extreme, proton-neutron ratios. In this article the authors discuss the latest advances in studying heavy nuclei. (author)

  9. 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…

  10. Force Factor Modulation in Electro Dynamic Loudspeakers

    DEFF Research Database (Denmark)

    Risbo, Lars; Agerkvist, Finn T.; Tinggaard, Carsten

    2016-01-01

    The relationship between the non-linear phenomenon of ’reluctance force’ and the position dependency of the voice coil inductance was established in 1949 by Cunningham, who called it ’magnetic attraction force’. This paper revisits Cunningham’s analysis and expands it into a generalised form...... that includes the frequency dependency and applies to coils with non-inductive (lossy) blocked impedance. The paper also demonstrates that Cunningham’s force can be explained physically as a modulation of the force factor which again is directly linked to modulation of the flux of the coil. A verification based...... on both experiments and simulations is presented along discussions of the impact of force factor modulation for various motor topologies. Finally, it is shown that the popular L2R2 coil impedance model does not correctly predict the force unless the new analysis is applied....

  11. 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.

  12. Water Orientation at Ceramide/Water Interfaces Studied by Heterodyne-Detected Vibrational Sum Frequency Generation Spectroscopy and Molecular Dynamics Simulation

    KAUST Repository

    Adhikari, Aniruddha

    2016-10-10

    Lipid/water interaction is essential for many biological processes. The water structure at the nonionic lipid interface remains little known, and there is no scope of a priori prediction of water orientation at nonionic interfaces, either. Here, we report our study combining advanced nonlinear spectroscopy and molecular dynamics simulation on the water orientation at the ceramide/water interface. We measured χ spectrum in the OH stretch region of ceramide/isotopically diluted water interface using heterodyne-detected vibrational sum-frequency generation spectroscopy and found that the interfacial water prefers an overall hydrogen-up orientation. Molecular dynamics simulation indicates that this preferred hydrogen-up orientation of water is determined by a delicate balance between hydrogen-up and hydrogen-down orientation induced by lipid-water and intralipid hydrogen bonds. This mechanism also suggests that water orientation at neutral lipid interfaces depends highly on the chemical structure of the lipid headgroup, in contrast to the charged lipid interfaces where the net water orientation is determined solely by the charge of the lipid headgroup.

  13. A modified synthetic driving force method for molecular dynamics simulation of grain boundary migration

    International Nuclear Information System (INIS)

    Yang, Liang; Li, Saiyi

    2015-01-01

    The synthetic driving force (SDF) molecular dynamics method, which imposes crystalline orientation-dependent driving forces for grain boundary (GB) migration, has been considered deficient in many cases. In this work, we revealed the cause of the deficiency and proposed a modified method by introducing a new technique to distinguish atoms in grains and GB such that the driving forces can be imposed properly. This technique utilizes cross-reference order parameter (CROP) to characterize local lattice orientations in a bicrystal and introduces a CROP-based definition of interface region to minimize interference from thermal fluctuations in distinguishing atoms. A validation of the modified method was conducted by applying it to simulate the migration behavior of Ni 〈1 0 0〉 and Al 〈1 1 2〉 symmetrical tilt GBs, in comparison with the original method. The discrepancies between the migration velocities predicted by the two methods are found to be proportional to their differences in distinguishing atoms. For the Al 〈1 1 2〉 GBs, the modified method predicts a negative misorientation dependency for both the driving pressure threshold for initiating GB movement and the mobility, which agree with experimental findings and other molecular dynamics computations but contradict those predicted using the original method. Last, the modified method was applied to evaluate the mobility of Ni Σ5 〈1 0 0〉 symmetrical tilt GB under different driving pressure and temperature conditions. The results reveal a strong driving pressure dependency of the mobility at relatively low temperatures and suggest that the driving pressure should be as low as possible but large enough to trigger continuous migration.

  14. Study of vapour phase dynamics with nitrogen boiling in the field of centrifugal forces

    International Nuclear Information System (INIS)

    Levchenko, N.M.; Kolod'ko, I.M.

    1987-01-01

    The vapour phase dynamics during film boiling of liquid nitrogen on horizontal wire in the field of centrifugal forces has been studied experimentally in a wide range of overloads(1 ≤ η ≤ 375) and heat fluxes (q kp2 ≤ q ≤ 4q kpi ). The available data confirmed and the theoretical relationships suggested make it possible to calculate the hydrodynamic film boiling parameters (wave length, bubble departure diameter and frequency) for other liquids

  15. Dynamic Time-Resolved Chirped-Pulse Rotational Spectroscopy of Vinyl Cyanide Photoproducts in a Room Temperature Flow Reactor

    Science.gov (United States)

    Zaleski, Daniel P.; Prozument, Kirill

    2017-06-01

    Chirped-pulsed (CP) Fourier transform rotational spectroscopy invented by Brooks Pate and coworkers a decade ago is an attractive tool for gas phase chemical dynamics and kinetics studies. A good reactor for such a purpose would have well-defined (and variable) temperature and pressure conditions to be amenable to accurate kinetic modeling. Furthermore, in low pressure samples with large enough number of molecular emitters, reaction dynamics can be observable directly, rather than mediated by supersonic expansion. In the present work, we are evaluating feasibility of in situ time-resolved CP spectroscopy in a room temperature flow tube reactor. Vinyl cyanide (CH_2CHCN), neat or mixed with inert gasses, flows through the reactor at pressures 1-50 μbar (0.76-38 mTorr) where it is photodissociated by a 193 nm laser. Millimeter-wave beam of the CP spectrometer co-propagates with the laser beam along the reactor tube and interacts with nascent photoproducts. Rotational transitions of HCN, HNC, and HCCCN are detected, with ≥10 μs time-steps for 500 ms following photolysis of CH_2CHCN. The post-photolysis evolution of the photoproducts' rotational line intensities is investigated for the effects of rotational and vibrational thermalization of energized photoproducts. Possible contributions from bimolecular and wall-mediated chemistry are evaluated as well.

  16. Mechanical, structural, and dynamical modifications of cholesterol exposed porcine aortic elastin.

    Science.gov (United States)

    Bilici, Kubra; Morgan, Steven W; Silverstein, Moshe C; Wang, Yunjie; Sun, Hyung Jin; Zhang, Yanhang; Boutis, Gregory S

    2016-11-01

    Elastin is a protein of the extracellular matrix that contributes significantly to the elasticity of connective tissues. In this study, we examine dynamical and structural modifications of aortic elastin exposed to cholesterol by NMR spectroscopic and relaxation methodologies. Macroscopic measurements are also presented and reveal that cholesterol treatment may cause a decrease in the stiffness of tissue. 2 H NMR relaxation techniques revealed differences between the relative populations of water that correlate with the swelling of the tissue following cholesterol exposure. 13 C magic-angle-spinning NMR spectroscopy and relaxation methods indicate that cholesterol treated aortic elastin is more mobile than control samples. Molecular dynamics simulations on a short elastin repeat VPGVG in the presence of cholesterol are used to investigate the energetic and entropic contributions to the retractive force, in comparison to the same peptide in water. Peptide stiffness is observed to reduce following cholesterol exposure due to a decrease in the entropic force. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Nuclear Dynamics of a Nearby Seyfert with NIRSpec Integral Field Spectroscopy

    Science.gov (United States)

    Bentz, Misty; Batiste, M.; Onken, C.; Roberts, C.; Valluri, M.; Vasiliev, E.

    2017-11-01

    Integral field spectroscopy has become an invaluable tool for investigating the physical conditions and dynamics deep inside galaxy nuclei. The integral field spectrograph on JWST provides some crucial advantages over those on AO- assisted ground-based telescopes like Gemini and VLT. In particular, JWST will provide a stable and diffraction limited point spread function (PSF) with no seeing halo, and the background will be significantly reduced resulting in shorter exposure times to achieve a benchmark signal-to-noise ratio, even for late-type galaxies that have shallower central cusps and fainter central surface brightnesses, and for which the exposure times required from the ground may be prohibitive. We are particularly interested in comparing black hole masses derived from the modeling of nuclear stellar dynamics to masses derived from reverberation mapping in the same galaxies. With this Early Release Science proposal, we request a small investment of time to clearly demonstrate JWST's capabilities in spatial and spectral resolution relative to the stringent technical requirements for direct black hole mass measurements. The technically demanding nature of the requisite measurements will allow us to explore the limits of what is possible to achieve with the NIRSpec IFU, thus providing technical guidance for a wide range of studies that seek to probe the physics of black hole feeding and feedback and their links to galaxy and black hole co-evolution.

  18. Theory and Applications of Solid-State NMR Spectroscopy to Biomembrane Structure and Dynamics

    Science.gov (United States)

    Xu, Xiaolin

    Solid-state Nuclear Magnetic Resonance (NMR) is one of the premiere biophysical methods that can be applied for addressing the structure and dynamics of biomolecules, including proteins, lipids, and nucleic acids. It illustrates the general problem of determining the average biomolecular structure, including the motional mean-square amplitudes and rates of the fluctuations. Lineshape and relaxtion studies give us a view into the molecular properties under different environments. To help the understanding of NMR theory, both lineshape and relaxation experiments are conducted with hexamethylbezene (HMB). This chemical compound with a simple structure serves as a perfect test molecule. Because of its highly symmetric structure, its motions are not very difficult to understand. The results for HMB set benchmarks for other more complicated systems like membrane proteins. After accumulating a large data set on HMB, we also proceed to develop a completely new method of data analysis, which yields the spectral densities in a body-fixed frame revealing internal motions of the system. Among the possible applications of solid-state NMR spectroscopy, we study the light activation mechanism of visual rhodopsin in lipid membranes. As a prototype of G-protein-coupled receptors, which are a large class of membrane proteins, the cofactor isomerization is triggered by photon absorption, and the local structural change is then propagated to a large-scale conformational change of the protein. Facilitation of the binding of transducin then passes along the visual signal to downstream effector proteins like transducin. To study this process, we introduce 2H labels into the rhodopsin chromophore retinal and the C-terminal peptide of transducin to probe the local structure and dynamics of these two hotspots of the rhodopsin activation process. In addition to the examination of local sites with solid-state 2H NMR spectroscopy, wide angle X-ray scattering (WAXS) provides us the chance of

  19. Time-resolved terahertz spectroscopy reveals the influence of charged sensitizing quantum dots on the electron dynamics in ZnO

    Czech Academy of Sciences Publication Activity Database

    Bamini, S.N.; Němec, Hynek; Žídek, Karel; Abdellah, M.; Al-Marri, M.J.; Chábera, P.; Ponseca, C.; Zheng, K.; Pullerits, T.

    2017-01-01

    Roč. 19, č. 8 (2017), s. 6006-6012 ISSN 1463-9076 R&D Projects: GA ČR GA17-03662S Institutional support: RVO:68378271 ; RVO:61389021 Keywords : sensitized semiconductors * ultrafast dynamics * terahertz spectroscopy Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics , supercond.) Impact factor: 4.123, year: 2016

  20. X-ray and photoelectron spectroscopy of light rare earths

    International Nuclear Information System (INIS)

    Fuggle, J.C.

    1983-01-01

    Core level photoelectron spectroscopy, X-ray absorption spectroscopy, bremsstrahlung isochromat spectroscopy and valence band studies are discussed. Particular emphasis is placed on cerium. Correlation effects, multiplet structure, screening effects and the dynamics of the processes involved are illustrated with selected examples. (Auth.)

  1. Dissociation mechanisms and dynamics of doubly charged CD3CN observed by PEPIPICO spectroscopy

    International Nuclear Information System (INIS)

    Harada, C.; Tada, S.; Yamamoto, K.; Senba, Y.; Yoshida, H.; Hiraya, A.; Wada, S.; Tanaka, K.; Tabayashi, K.

    2006-01-01

    Dissociation of free acetonitrile-d 3 molecule, CD 3 CN induced by core level excitation was studied near the nitrogen K-edge by time-of-flight fragment mass spectroscopy. A variety of atomic and molecular fragment cations such as D + , CD n + , C 2 D n + , and CD n CN + were detected using the effusive CD 3 CN beam. Photoelectron-photoion-photoion coincidence technique was applied to analyse the dissociation mechanisms and dynamics of doubly charged CD 3 CN 2+ following the N(1s-π * ) excitation. The charge separation mechanisms of core-excited CD 3 CN were discussed in connection with Auger final state distributions

  2. Multi-MHz micro-electro-mechanical sensors for atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Legrand, Bernard, E-mail: bernard.legrand@laas.fr [LAAS-CNRS, Université de Toulouse, CNRS, 7 avenue du colonel Roche, F-31400 Toulouse (France); Salvetat, Jean-Paul [CRPP, 115 avenue Schweitzer, F-33600 Pessac (France); Walter, Benjamin; Faucher, Marc; Théron, Didier [IEMN, avenue Henri Poincaré, F-59652 Villeneuve d’Ascq (France); Aimé, Jean-Pierre [CBMN, allée Geoffroy Saint Hilaire, Bât. B14, F-33600 Pessac (France)

    2017-04-15

    Silicon ring-shaped micro-electro-mechanical resonators have been fabricated and used as probes for dynamic atomic force microscopy (AFM) experiments. They offer resotnance frequency above 10 MHz, which is notably greater than that of usual cantilevers and quartz-based AFM probes. On-chip electrical actuation and readout of the tip oscillation are obtained by means of built-in capacitive transducers. Displacement and force resolutions have been determined from noise analysis at 1.5 fm/√Hz and 0.4 pN/√Hz, respectively. Despite the high effective stiffness of the probes, the tip-surface interaction force is kept below 1 nN by using vibration amplitude significantly below 100 pm and setpoint close to the free vibration conditions. Imaging capabilities in amplitude- and frequency-modulation AFM modes have been demonstrated on block copolymer surfaces. Z-spectroscopy experiments revealed that the tip is vibrating in permanent contact with the viscoelastic material, with a pinned contact line. Results are compared to those obtained with commercial AFM cantilevers driven at large amplitudes (>10 nm). - Highlights: • Silicon MEMS resonators are used as AFM probes above 10 MHz. • Integrated capacitive transducers drive and sense sub-nanometer tip oscillation. • Force resolution is below 1 pN/√Hz. • Block copolymer surface is imaged using AM and FM AFM modes. • Probes are operated at small vibration amplitude in permanent viscoelastic contact.

  3. Multi-MHz micro-electro-mechanical sensors for atomic force microscopy

    International Nuclear Information System (INIS)

    Legrand, Bernard; Salvetat, Jean-Paul; Walter, Benjamin; Faucher, Marc; Théron, Didier; Aimé, Jean-Pierre

    2017-01-01

    Silicon ring-shaped micro-electro-mechanical resonators have been fabricated and used as probes for dynamic atomic force microscopy (AFM) experiments. They offer resotnance frequency above 10 MHz, which is notably greater than that of usual cantilevers and quartz-based AFM probes. On-chip electrical actuation and readout of the tip oscillation are obtained by means of built-in capacitive transducers. Displacement and force resolutions have been determined from noise analysis at 1.5 fm/√Hz and 0.4 pN/√Hz, respectively. Despite the high effective stiffness of the probes, the tip-surface interaction force is kept below 1 nN by using vibration amplitude significantly below 100 pm and setpoint close to the free vibration conditions. Imaging capabilities in amplitude- and frequency-modulation AFM modes have been demonstrated on block copolymer surfaces. Z-spectroscopy experiments revealed that the tip is vibrating in permanent contact with the viscoelastic material, with a pinned contact line. Results are compared to those obtained with commercial AFM cantilevers driven at large amplitudes (>10 nm). - Highlights: • Silicon MEMS resonators are used as AFM probes above 10 MHz. • Integrated capacitive transducers drive and sense sub-nanometer tip oscillation. • Force resolution is below 1 pN/√Hz. • Block copolymer surface is imaged using AM and FM AFM modes. • Probes are operated at small vibration amplitude in permanent viscoelastic contact.

  4. Characterization of the disruption of neural control strategies for dynamic fingertip forces from attractor reconstruction.

    Directory of Open Access Journals (Sweden)

    Lorenzo Peppoloni

    Full Text Available The Strength-Dexterity (SD test measures the ability of the pulps of the thumb and index finger to compress a compliant and slender spring prone to buckling at low forces (<3N. We know that factors such as aging and neurodegenerative conditions bring deteriorating physiological changes (e.g., at the level of motor cortex, cerebellum, and basal ganglia, which lead to an overall loss of dexterous ability. However, little is known about how these changes reflect upon the dynamics of the underlying biological system. The spring-hand system exhibits nonlinear dynamical behavior and here we characterize the dynamical behavior of the phase portraits using attractor reconstruction. Thirty participants performed the SD test: 10 young adults, 10 older adults, and 10 older adults with Parkinson's disease (PD. We used delayed embedding of the applied force to reconstruct its attractor. We characterized the distribution of points of the phase portraits by their density (number of distant points and interquartile range and geometric features (trajectory length and size. We find phase portraits from older adults exhibit more distant points (p = 0.028 than young adults and participants with PD have larger interquartile ranges (p = 0.001, trajectory lengths (p = 0.005, and size (p = 0.003 than their healthy counterparts. The increased size of the phase portraits with healthy aging suggests a change in the dynamical properties of the system, which may represent a weakening of the neural control strategy. In contrast, the distortion of the attractor in PD suggests a fundamental change in the underlying biological system, and disruption of the neural control strategy. This ability to detect differences in the biological mechanisms of dexterity in healthy and pathological aging provides a simple means to assess their disruption in neurodegenerative conditions and justifies further studies to understand the link with the physiological changes.

  5. Rapid and serial quantification of adhesion forces of yeast and Mammalian cells.

    Directory of Open Access Journals (Sweden)

    Eva Potthoff

    Full Text Available Cell adhesion to surfaces represents the basis for niche colonization and survival. Here we establish serial quantification of adhesion forces of different cell types using a single probe. The pace of single-cell force-spectroscopy was accelerated to up to 200 yeast and 20 mammalian cells per probe when replacing the conventional cell trapping cantilever chemistry of atomic force microscopy by underpressure immobilization with fluidic force microscopy (FluidFM. In consequence, statistically relevant data could be recorded in a rapid manner, the spectrum of examinable cells was enlarged, and the cell physiology preserved until approached for force spectroscopy. Adhesion forces of Candida albicans increased from below 4 up to 16 nN at 37°C on hydrophobic surfaces, whereas a Δhgc1-mutant showed forces consistently below 4 nN. Monitoring adhesion of mammalian cells revealed mean adhesion forces of 600 nN of HeLa cells on fibronectin and were one order of magnitude higher than those observed for HEK cells.

  6. Slow dynamics in an azopolymer molecular layer studied by x-ray photon correlation spectroscopy

    International Nuclear Information System (INIS)

    Orsi, D.; Fluerasu, A.; Cristofolini, L.; Fontana, M.P.; Pontecorvo, E.; Caronna, C.; Zontone, F.; Madsen, A.

    2010-01-01

    We report the results of x-ray photon correlation spectroscopy (XPCS) experiments on multilayers of a photosensitive azo-polymer which can be softened by photoisomerization. Time correlation functions have been measured at different temperatures and momentum transfers (q) and under different illumination conditions (dark, UV or visible). The correlation functions are well described by the Kohlrausch-Williams-Watts (KWW) form with relaxation times that are proportional to q -1 . The characteristic relaxation times follow the same Vogel-Fulcher-Tammann law describing the bulk viscosity of this polymer. The out-of-equilibrium relaxation dynamics following a UV photoperturbation are accelerated, which is in agreement with a fluidification effect previously measured by rheology. The transient dynamics are characterized by two times correlation function, and dynamical heterogeneity is evidenced by calculating the variance χ of the degree of correlation as a function of ageing time. A clear peak in χ appears at a well defined time τ C which scales with q -1 and with the ageing time, in a similar fashion as previously reported in colloidal suspensions (O. Dauchot et al. Phys. Rev. Lett. 95 265701 (2005)). From an accurate analysis of the correlation functions we could demonstrate a temperature and light dependent cross-over from compressed KWW to simple exponential behavior.

  7. Velocity Potential in Engineering Hydraulics versus Force Potential in Groundwater Dynamics

    Science.gov (United States)

    Weyer, K.

    2013-12-01

    required to overcome the resistance to downward flow in penetrated rocks. As one of the consequences, the engineering hydraulics concept of buoyancy forces does not comply with physics. In general the vectorial forces within gravitationally-driven flow systems are ignored when using engineering hydraulics. Scheidegger (1974, p. 79) states, however, verbatim and unequivocally: 'It is thus a force potential and not a velocity potential which governs flow through porous media' (emphasis added). This presentation will outline the proper forces for groundwater flow and their calculations based on Hubbert's force potential and additional physical insights by Weyer (1978). REFERENCES Bear, J. 1972. Dynamics of Fluids in Porous Media. American Elsevier Publishing Company, Inc., New York, NY, USA. de Marsily, G. 1986. Quantitative Hydrogeology: Groundwater Hydrology for Engineers. Academic Press, San Diego, California, USA. Hubbert, M.K. 1940. The theory of groundwater motion. Journal of Geology 48(8): 785-944. Muskat, Morris, 1937. The flow of homogeneous fluids through porous media. McGraw-Hill Book Company Inc., New York, NY, USA Scheidegger. A.E., 1974. The physics of flow through permeable media. Third Edition. University of Toronto Press, Toronto, Ontario, Canada Weyer, K.U., 1978. Hydraulic forces in permeable media. Bulletin du B.R.G.M., Vol. 91, pp. 286-297, Orléans, France.

  8. MDM2-MDM4 molecular interaction investigated by atomic force spectroscopy and surface plasmon resonance.

    Science.gov (United States)

    Moscetti, Ilaria; Teveroni, Emanuela; Moretti, Fabiola; Bizzarri, Anna Rita; Cannistraro, Salvatore

    Murine double minute 2 (MDM2) and 4 (MDM4) are known as the main negative regulators of p53, a tumor suppressor. They are able to form heterodimers that are much more effective in the downregulation of p53. Therefore, the MDM2-MDM4 complex could be a target for promising therapeutic restoration of p53 function. To this aim, a deeper understanding of the molecular mechanisms underlining the heterodimerization is needed. The kinetic and thermodynamic characterization of the MDM2-MDM4 complex was performed with two complementary approaches: atomic force spectroscopy and surface plasmon resonance. Both techniques revealed an equilibrium dissociation constant (KD ) in the micromolar range for the MDM2-MDM4 heterodimer, similar to related complexes involved in the p53 network. Furthermore, the MDM2-MDM4 complex is characterized by a relatively high free energy, through a single energy barrier, and by a lifetime in the order of tens of seconds. New insights into the MDM2-MDM4 interaction could be highly important for developing innovative anticancer drugs focused on p53 reactivation.

  9. Three-nucleon forces

    International Nuclear Information System (INIS)

    Sauer, P.U.

    2014-01-01

    In this paper, the role of three-nucleon forces in ab initio calculations of nuclear systems is investigated. The difference between genuine and induced many-nucleon forces is emphasized. Induced forces arise in the process of solving the nuclear many-body problem as technical intermediaries toward calculationally converged results. Genuine forces make up the Hamiltonian. They represent the chosen underlying dynamics. The hierarchy of contributions arising from genuine two-, three- and many-nucleon forces is discussed. Signals for the need of the inclusion of genuine three-nucleon forces are studied in nuclear systems, technically best under control, especially in three-nucleon and four-nucleon systems. Genuine three-nucleon forces are important for details in the description of some observables. Their contributions to observables are small on the scale set by two-nucleon forces. (author)

  10. Comparing localized and nonlocalized dynamic 31P magnetic resonance spectroscopy in exercising muscle at 7T

    Science.gov (United States)

    Meyerspeer, Martin; Robinson, Simon; Nabuurs, Christine I; Scheenen, Tom; Schoisengeier, Adrian; Unger, Ewald; Kemp, Graham J; Moser, Ewald

    2012-01-01

    By improving spatial and anatomical specificity, localized spectroscopy can enhance the power and accuracy of the quantitative analysis of cellular metabolism and bioenergetics. Localized and nonlocalized dynamic 31P magnetic resonance spectroscopy using a surface coil was compared during aerobic exercise and recovery of human calf muscle. For localization, a short echo time single-voxel magnetic resonance spectroscopy sequence with adiabatic refocusing (semi-LASER) was applied, enabling the quantification of phosphocreatine, inorganic phosphate, and pH value in a single muscle (medial gastrocnemius) in single shots (TR = 6 s). All measurements were performed in a 7 T whole body scanner with a nonmagnetic ergometer. From a series of equal exercise bouts we conclude that: (a) with localization, measured phosphocreatine declines in exercise to a lower value (79 ± 7% cf. 53 ± 10%, P = 0.002), (b) phosphocreatine recovery shows shorter half time (t1/2 = 34 ± 7 s cf. t1/2 = 42 ± 7 s, nonsignificant) and initial postexercise phosphocreatine resynthesis rate is significantly higher (32 ± 5 mM/min cf. 17 ± 4 mM/min, P = 0.001) and (c) in contrast to nonlocalized 31P magnetic resonance spectroscopy, no splitting of the inorganic phosphate peak is observed during exercise or recovery, just an increase in line width during exercise. This confirms the absence of contaminating signals originating from weaker-exercising muscle, while an observed inorganic phosphate line broadening most probably reflects variations across fibers in a single muscle. Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc. PMID:22334374

  11. Time-resolved spectroscopy of the probe fluorescence in the study of human blood protein dynamic structure on SR beam

    International Nuclear Information System (INIS)

    Dobretsov, G.E.; Kurek, N.K.; Syrejshchikova, T.I.; Yakimenko, M.N.; Clarke, D.T.; Jones, G.R.; Munro, I.H.

    2000-01-01

    Time-resolved spectroscopy on the SRS of the Daresbury Laboratory was used for the study of the human serum lipoproteins and human blood albumins with fluorescent probes K-37 and K-35, developed in Russia. The probe K-37 was found sensitive to the difference in dynamic properties of the lipid objects. Two sets of the parameters were used for the description of lipid dynamic structure: (1) time-resolved fluorescence spectra and (2) time-resolved fluorescence depolarization as a function of rotational mobility of lipid molecules. Each measured dynamic parameter reflected the monotonous changes of dynamic properties in the range: lipid spheres-very low density lipoproteins-low density lipoproteins-high density lipoproteins-phospholipid liposomes. The range is characterized by the increase of the ratio polar/ nonpolar lipids. Thus, time-resolved fluorescence could be used to detect some structural modifications in lipoproteins related to atherosclerosis and subsequent cardiovascular diseases development

  12. Surface vibrational spectroscopy

    International Nuclear Information System (INIS)

    Erskine, J.L.

    1984-01-01

    A brief review of recent studies which combine measurements of surface vibrational energies with lattice dynamical calculations is presented. These results suggest that surface vibrational spectroscopy offers interesting prospects for use as a molecular-level probe of surface geometry, adsorbate bond distances and molecular orientations

  13. Dynamic calibration and validation of an accelerometer force balance for hypersonic lifting models.

    Science.gov (United States)

    Singh, Prakash; Trivedi, Sharad; Menezes, Viren; Hosseini, Hamid

    2014-01-01

    An accelerometer-based force balance was designed and developed for the measurement of drag, lift, and rolling moment on a blunt-nosed, flapped delta wing in a short-duration hypersonic shock tunnel. Calibration and validation of the balance were carried out by a convolution technique using hammer pulse test and surface pressure measurements. In the hammer pulse test, a known impulse was applied to the model in the appropriate direction using an impulse hammer, and the corresponding output of the balance (acceleration) was recorded. Fast Fourier Transform (FFT) was operated on the output of the balance to generate a system response function, relating the signal output to the corresponding load input. Impulse response functions for three components of the balance, namely, axial, normal, and angular, were obtained for a range of input load. The angular system response function was corresponding to rolling of the model. The impulse response functions thus obtained, through dynamic calibration, were operated on the output (signals) of the balance under hypersonic aerodynamic loading conditions in the tunnel to get the time history of the unknown aerodynamic forces and moments acting on the model. Surface pressure measurements were carried out on the model using high frequency pressure transducers, and forces and moments were deduced thereon. Tests were carried out at model angles of incidence of 0, 5, 10, and 15 degrees. A good agreement was observed among the results of different experimental methods. The balance developed is a comprehensive force/moment measurement device that can be used on complex, lifting, aerodynamic geometries in ground-based hypersonic test facilities.

  14. Enhanced intermolecular forces in supramolecular polymer nanocomposites

    Directory of Open Access Journals (Sweden)

    F. Lin

    2017-09-01

    Full Text Available Ureido-pyrimidone (Upy can dimerize in a self-complementary array of quadruple hydrogen bonds. In this paper, supramolecular polymer composites were prepared by blending Upy functionalized nanosilica with Upy end-capped polycarbonatediol. Surface characteristics of Upy functionalized nanosilica and influences of supramolecular forces on interfacial binding were researched. Fourier transform infrared spectroscopy (FTIR, Nuclear magnetic resonance (NMR and Gel permeation chromatography (GPC were used to characterize the synthesized molecules. Grafting ratio of Upy segments on the surface of nanosilica was analysed by Thermogravimetic analysis (TGA. Hydrophobicity and morphology of Upy modified nanosilica were analysed by Contact angle tester and Scanning electron microscope (SEM. Furthermore, dynamic thermo mechanical properties, mechanical properties and distribution of nanosilica in supramolecular polymer composites were also researched. Compared with the matrix resin, tensile stress and young's modulus of supramolecular polymer composites containing 5 wt% modified nanosilica were increased by 292 and 198% respectively.

  15. Investigation of the spectroscopy and relaxation dynamics of benzaldehyde using molecular orbital calculations and laser ionization time-of-flight mass spectroscopy

    Science.gov (United States)

    da Silva, Maria Cristina Rodrigues

    1998-11-01

    Molecular orbital methods and laser ionization mass spectrometry measurements are used to investigate the spectroscopy and relaxation dynamics of benzaldehyde following excitation to its S2(/pi/pi/sp/*) state. Energies, equilibrium geometries and vibrational frequencies of ground and low-lying excited states of benzaldehyde neutral and cation determined by ab initio calculations provide a theoretical description of the electronic spectroscopy of benzaldehyde and of the changes occurring on excitation and ionization. The S2(/pi/pi/sp/*)[/gets]S0 excitation spectrum of jet-cooled benzaldehyde acquired using two-color laser ionization mass spectrometry techniques is interpreted with the aid of these calculations. The spectrum is dominated by the origin band and by transitions involving some of the ring modes consistent with the results of the molecular orbital calculations that indicate that the major geometric changes on excitation to S2 are located in the aromatic ring. Ten fundamental vibrations of the S2(/pi/pi/sp/*) state are assigned. The dissociation dynamics of benzaldehyde into benzene and carbon monoxide following excitation to its S2(/pi/pi/sp/*) state are investigated under jet- cooled conditions by two-color laser ionization mass spectrometry using a pump-probe technique. This experimental arrangement allows monitoring the benzaldehyde reactant and the benzene product ion signals as a function of the time delay between the excitation and ionization steps. A kinetic model is proposed to explain the observed biexponential decay of the benzaldehyde signal and the single exponential growth of the benzene product signal in terms of a sequential decay of two excited states of benzaldehyde, one of which leads to formation of benzene molecules in its lowest triplet state. Reactant disappearance and product appearance rates are determined for a number of vibronic transitions of the S2 state. They are found to increase with excitation energy without any indication

  16. A review of a method for dynamic load distribution, dynamic modeling, and explicit internal force control when two serial link manipulators mutually lift and transport a rigid body object

    International Nuclear Information System (INIS)

    Unseren, M.A.

    1997-09-01

    The report reviews a method for modeling and controlling two serial link manipulators which mutually lift and transport a rigid body object in a three dimensional workspace. A new vector variable is introduced which parameterizes the internal contact force controlled degrees of freedom. A technique for dynamically distributing the payload between the manipulators is suggested which yields a family of solutions for the contact forces and torques the manipulators impart to the object. A set of rigid body kinematic constraints which restricts the values of the joint velocities of both manipulators is derived. A rigid body dynamical model for the closed chain system is first developed in the joint space. The model is obtained by generalizing the previous methods for deriving the model. The joint velocity and acceleration variables in the model are expressed in terms of independent pseudovariables. The pseudospace model is transformed to obtain reduced order equations of motion and a separate set of equations governing the internal components of the contact forces and torques. A theoretic control architecture is suggested which explicitly decouples the two sets of equations comprising the model. The controller enables the designer to develop independent, non-interacting control laws for the position control and internal force control of the system

  17. A review of a method for dynamic load distribution, dynamic modeling, and explicit internal force control when two serial link manipulators mutually lift and transport a rigid body object

    Energy Technology Data Exchange (ETDEWEB)

    Unseren, M.A.

    1997-09-01

    The report reviews a method for modeling and controlling two serial link manipulators which mutually lift and transport a rigid body object in a three dimensional workspace. A new vector variable is introduced which parameterizes the internal contact force controlled degrees of freedom. A technique for dynamically distributing the payload between the manipulators is suggested which yields a family of solutions for the contact forces and torques the manipulators impart to the object. A set of rigid body kinematic constraints which restricts the values of the joint velocities of both manipulators is derived. A rigid body dynamical model for the closed chain system is first developed in the joint space. The model is obtained by generalizing the previous methods for deriving the model. The joint velocity and acceleration variables in the model are expressed in terms of independent pseudovariables. The pseudospace model is transformed to obtain reduced order equations of motion and a separate set of equations governing the internal components of the contact forces and torques. A theoretic control architecture is suggested which explicitly decouples the two sets of equations comprising the model. The controller enables the designer to develop independent, non-interacting control laws for the position control and internal force control of the system.

  18. Interaction of VUV-photons with molecules. Spectroscopy and dynamics of molecular superexcited states

    International Nuclear Information System (INIS)

    Hatano, Y.

    2002-01-01

    Complete text of publication follows. A survey is given of recent progress in experimental studies of the interaction of VUV-photons with molecules, i.e., those of photoabsorption, photoionization, and photodissociation of molecules in the excitation photon energy range of 10-50 eV, with a particular emphasis placed on current understanding of the spectroscopy and dynamics of formed molecular superexcited states. These studies are of great importance in understanding the interaction of ionizing radiation with matter. Molecules studied are ranged from simple diatomic and triatomic molecules to polyatomic molecules such as hydrocarbons. Most of the observed molecular superexcited states are assigned to high Rydber states which are vibrationally, doubly, or inner-core excited and converge to each of ion states. Non-Rydberg superexcited states are also observed. Dissociation into neutral fragments in comparison with ionization is of unexpectedly great importance in the observed decay of each of these state-assigned superexcited molecules. Dissociation dynamics as well as its products of superexcited states are remarkably different from those of lower excited states below about ionization thresholds. Some remarks are also presented of molecules in the condensed phase

  19. 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...

  20. Development of force-detected THz-ESR measurement system and its application to metal porphyrin complexes

    Science.gov (United States)

    Takahashi, Hideyuki; Okamoto, Tsubasa; Ohmichi, Eiji; Ohta, Hitoshi

    Electron spin resonance spectroscopy in the terahertz region (THz-ESR) is a promising technique to study biological materials such as metalloproteins because it directly probes the metal ion sites that play an important role in the emergence of functionality. By combining THz-ESR with force detection, the samples mass is reduced to the order of ng. This feature is of great advantage because the sample preparation process of biological materials is time-consuming. We developed a force-detected THz-ESR system utilizing optical interferometry for precise cantilever displacement measurement. In order to suppress the sensitivity fluctuation and instability of cantilever dynamics under high magnetic field, the tuning of interferometer is feedback-controlled during a measurement. By using this system, we successfully observed the ESR signal of hemin, which is a model substance of hemoglobin and myoglobin, in THz region.

  1. Studies of the relationship between environmental forcing and the structure and dynamics of tornado-like vortices; TOPICAL

    International Nuclear Information System (INIS)

    Nolan, David S.; Almgren, Ann S.; Bell, John B.

    2000-01-01

    Axisymmetric numerical simulations continue to provide insight into how the structure, dynamics, and maximum wind speeds of tornadoes, and other convectively-maintained vortices, are influenced by the surrounding environment. This work is continued with a new numerical model of axisymmetric incompressible flow that incorporates adaptive mesh refinement. The model dynamically increases or decreases the resolution in regions of interest as determined by a specified refinement criterion. Here, the criterion used is based on the cell Reynolds number dx dv / nu, so that the flow is guaranteed to be laminar on the scale of the local grid spacing. The model is used to investigate how the altitude and shape of the convective forcing, the size of the domain, and the effective Reynolds number (based on the choice of the eddy viscosity nu) influence the structure and dynamics of the vortex. Over a wide variety of domain and forcing geometries,the vortex Reynolds number Gamma / nu (the ratio of the far-field circulation to the eddy viscosity) is shown to be the most important parameter for determining vortex structure and behavior. Furthermore,it is found that the vertical scale of the convective forcing only affects the vortex inasmuch as this vertical scale contributes to the total strength of the convective forcing. The horizontal scale of the convective forcing, however, is found to be the fundamental length scale in the problem, in that it can determine both the circulation of the fluid that is drawn into the vortex core, and also influences the depth of the swirling boundary layer. Higher mean wind speeds are sustained as the eddy viscosity is decreased; however, it is observed that the highest wind speeds are found in the high-swirl, two-celled vortex regime rather than in the low-swirl, one-celled regime, which is in contrast with some previous results. The conclusions drawn from these results are applied to dimensional simulations with scales similar to the

  2. Detection Limits of DLS and UV-Vis Spectroscopy in Characterization of Polydisperse Nanoparticles Colloids

    Directory of Open Access Journals (Sweden)

    Emilia Tomaszewska

    2013-01-01

    Full Text Available Dynamic light scattering is a method that depends on the interaction of light with particles. This method can be used for measurements of narrow particle size distributions especially in the range of 2–500 nm. Sample polydispersity can distort the results, and we could not see the real populations of particles because big particles presented in the sample can screen smaller ones. Although the theory and mathematical basics of DLS technique are already well known, little has been done to determine its limits experimentally. The size and size distribution of artificially prepared polydisperse silver nanoparticles (NPs colloids were studied using dynamic light scattering (DLS and ultraviolet-visible (UV-Vis spectroscopy. Polydisperse colloids were prepared based on the mixture of chemically synthesized monodisperse colloids well characterized by atomic force microscopy (AFM, transmission electron microscopy (TEM, DLS, and UV-Vis spectroscopy. Analysis of the DLS results obtained for polydisperse colloids reveals that several percent of the volume content of bigger NPs could screen completely the presence of smaller ones. The presented results could be extremely important from nanoparticles metrology point of view and should help to understand experimental data especially for the one who works with DLS and/or UV-Vis only.

  3. Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations.

    Science.gov (United States)

    Watts, Charles R; Gregory, Andrew; Frisbie, Cole; Lovas, Sándor

    2018-03-01

    The conformational space and structural ensembles of amyloid beta (Aβ) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α-helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of β-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected β-sheet-turn-β-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different. © 2017 Wiley Periodicals, Inc.

  4. Exciton–vibrational coupling in the dynamics and spectroscopy of Frenkel excitons in molecular aggregates

    International Nuclear Information System (INIS)

    Schröter, M.; Ivanov, S.D.; Schulze, J.; Polyutov, S.P.; Yan, Y.; Pullerits, T.; Kühn, O.

    2015-01-01

    The influence of exciton–vibrational coupling on the optical and transport properties of molecular aggregates is an old problem that gained renewed interest in recent years. On the experimental side, various nonlinear spectroscopic techniques gave insight into the dynamics of systems as complex as photosynthetic antennae. Striking evidence was gathered that in these protein–pigment complexes quantum coherence is operative even at room temperature conditions. Investigations were triggered to understand the role of vibrational degrees of freedom, beyond that of a heat bath characterized by thermal fluctuations. This development was paralleled by theory, where efficient methods emerged, which could provide the proper frame to perform non-Markovian and non-perturbative simulations of exciton–vibrational dynamics and spectroscopy. This review summarizes the state of affairs of the theory of exciton–vibrational interaction in molecular aggregates and photosynthetic antenna complexes. The focus is put on the discussion of basic effects of exciton–vibrational interaction from the stationary and dynamics points of view. Here, the molecular dimer plays a prominent role as it permits a systematic investigation of absorption and emission spectra by numerical diagonalization of the exciton–vibrational Hamiltonian in a truncated Hilbert space. An extension to larger aggregates, having many coupled nuclear degrees of freedom, becomes possible with the Multi-Layer Multi-Configuration Time-Dependent Hartree (ML-MCTDH) method for wave packet propagation. In fact it will be shown that this method allows one to approach the limit of almost continuous spectral densities, which is usually the realm of density matrix theory. Real system–bath situations are introduced for two models, which differ in the way strongly coupled nuclear coordinates are treated, as a part of the relevant system or the bath. A rather detailed exposition of the Hierarchy Equations Of Motion (HEOM

  5. Simultaneous current, force and dissipation measurements on the Si(111 7×7 surface with an optimized qPlus AFM/STM technique

    Directory of Open Access Journals (Sweden)

    Zsolt Majzik

    2012-03-01

    Full Text Available We present the results of simultaneous scanning-tunneling and frequency-modulated dynamic atomic force microscopy measurements with a qPlus setup. The qPlus sensor is a purely electrical sensor based on a quartz tuning fork. If both the tunneling current and the force signal are to be measured at the tip, a cross-talk of the tunneling current with the force signal can easily occur. The origin and general features of the capacitive cross-talk will be discussed in detail in this contribution. Furthermore, we describe an experimental setup that improves the level of decoupling between the tunneling-current and the deflection signal. The efficiency of this experimental setup is demonstrated through topography and site-specific force/tunneling-spectroscopy measurements on the Si(111 7×7 surface. The results show an excellent agreement with previously reported data measured by optical interferometric deflection.

  6. Use of ultrafast dispersed pump-dump-probe and pump-repump-probe spectroscopies to explore the light-induced dynamics of peridinin in solution

    NARCIS (Netherlands)

    Papagiannakis, E.; Vengris, M.; Larsen, D.S.; van Stokkum, I.H.M.; Hiller, R.G.; van Grondelle, R.

    2006-01-01

    Optical pump-induced dynamics of the highly asymmetric carotenoid peridinin in methanol was studied by dispersed pump-probe, pump-dump-probe, and pump-repump-probe transient absorption spectroscopy in the visible region. Dispersed pump-probe measurements show that the decay of the initially excited

  7. Karhunen-Loève treatment to remove noise and facilitate data analysis in sensing, spectroscopy and other applications.

    Science.gov (United States)

    Zaharov, V V; Farahi, R H; Snyder, P J; Davison, B H; Passian, A

    2014-11-21

    Resolving weak spectral variations in the dynamic response of materials that are either dominated or excited by stochastic processes remains a challenge. Responses that are thermal in origin are particularly relevant examples due to the delocalized nature of heat. Despite its inherent properties in dealing with stochastic processes, the Karhunen-Loève expansion has not been fully exploited in measurement of systems that are driven solely by random forces or can exhibit large thermally driven random fluctuations. Here, we present experimental results and analysis of the archetypes (a) the resonant excitation and transient response of an atomic force microscope probe by the ambient random fluctuations and nanoscale photothermal sample response, and (b) the photothermally scattered photons in pump-probe spectroscopy. In each case, the dynamic process is represented as an infinite series with random coefficients to obtain pertinent frequency shifts and spectral peaks and demonstrate spectral enhancement for a set of compounds including the spectrally complex biomass. The considered cases find important applications in nanoscale material characterization, biosensing, and spectral identification of biological and chemical agents.

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

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Gaigong [Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Lin, Lin, E-mail: linlin@math.berkeley.edu [Department of Mathematics, University of California, Berkeley, Berkeley, CA 94720 (United States); Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Hu, Wei, E-mail: whu@lbl.gov [Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Yang, Chao, E-mail: cyang@lbl.gov [Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Pask, John E., E-mail: pask1@llnl.gov [Physics Division, Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States)

    2017-04-15

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

  9. Frontiers in Fluctuation Spectroscopy: Measuring protein dynamics and protein spatio-temporal connectivity

    Science.gov (United States)

    Digman, Michelle

    Fluorescence fluctuation spectroscopy has evolved from single point detection of molecular diffusion to a family of microscopy imaging correlation tools (i.e. ICS, RICS, STICS, and kICS) useful in deriving spatial-temporal dynamics of proteins in living cells The advantage of the imaging techniques is the simultaneous measurement of all points in an image with a frame rate that is increasingly becoming faster with better sensitivity cameras and new microscopy modalities such as the sheet illumination technique. A new frontier in this area is now emerging towards a high level of mapping diffusion rates and protein dynamics in the 2 and 3 dimensions. In this talk, I will discuss the evolution of fluctuation analysis from the single point source to mapping diffusion in whole cells and the technology behind this technique. In particular, new methods of analysis exploit correlation of molecular fluctuations originating from measurement of fluctuation correlations at distant points (pair correlation analysis) and methods that exploit spatial averaging of fluctuations in small regions (iMSD). For example the pair correlation fluctuation (pCF) analyses done between adjacent pixels in all possible radial directions provide a window into anisotropic molecular diffusion. Similar to the connectivity atlas of neuronal connections from the MRI diffusion tensor imaging these new tools will be used to map the connectome of protein diffusion in living cells. For biological reaction-diffusion systems, live single cell spatial-temporal analysis of protein dynamics provides a mean to observe stochastic biochemical signaling in the context of the intracellular environment which may lead to better understanding of cancer cell invasion, stem cell differentiation and other fundamental biological processes. National Institutes of Health Grant P41-RRO3155.

  10. Dynamic analyses of electromagnetic force on ferritic board for AMTEX on JFT-2M

    Energy Technology Data Exchange (ETDEWEB)

    Urata, K. E-mail: uratak@fusion.naka.jaeri.go.jp; Suzuki, Y.; Kudough, F.; Kimura, H.; Miura, Y.; Yamamoto, M

    2001-10-01

    Covering the inside wall of the vacuum vessel with the ferritic boards (FBs) is planned in the third stage of the Advanced Material Tokamak Experiment (AMTEX) on JFT-2M. The total magnetic forces induced on FBs were calculated by the three-dimensional dynamic electromagnetic field analysis code, EMSolution, with solid magnetic elements to consider the coupled effects of eddy current and magnetization, and the skin effect of eddy current. The structural integrity was evaluated on the bolts fixing the FBs to the vacuum vessel.

  11. Dynamic analyses of electromagnetic force on ferritic board for AMTEX on JFT-2M

    International Nuclear Information System (INIS)

    Urata, K.; Suzuki, Y.; Kudough, F.; Kimura, H.; Miura, Y.; Yamamoto, M.

    2001-01-01

    Covering the inside wall of the vacuum vessel with the ferritic boards (FBs) is planned in the third stage of the Advanced Material Tokamak Experiment (AMTEX) on JFT-2M. The total magnetic forces induced on FBs were calculated by the three-dimensional dynamic electromagnetic field analysis code, EMSolution, with solid magnetic elements to consider the coupled effects of eddy current and magnetization, and the skin effect of eddy current. The structural integrity was evaluated on the bolts fixing the FBs to the vacuum vessel

  12. Trends in mica–mica adhesion reflect the influence of molecular details on long-range dispersion forces underlying aggregation and coalignment

    Energy Technology Data Exchange (ETDEWEB)

    Li, Dongsheng; Chun, Jaehun; Xiao, Dongdong; Zhou, Weijiang; Cai, Huacheng; Zhang, Lei; Rosso, Kevin M.; Mundy, Christopher J.; Schenter, Gregory K.; De Yoreo, James J.

    2017-07-05

    Oriented attachment of nanocrystalline subunits is recognized as a common crystallization pathway that is closely related to formation of nanoparticle superlattices, mesocrystals, and other kinetically stabilized structures. Approaching particles have been observed to rotate to achieve co-alignment while separated by nanometer-scale solvent layers. Little is known about the forces that drive co-alignment, particularly in this “solvent-separated” regime. To obtain a mechanistic understanding of this process, we used atomic force microscopy-based dynamic force spectroscopy with tips fabricated from oriented mica to measure the adhesion forces between mica (001) surfaces in electrolyte solutions as a function of orientation, temperature, electrolyte type, and electrolyte concentration. The results reveal a ~60° periodicity as well as a complex dependence on electrolyte concentration and temperature. A continuum model that considers the competition between electrostatic repulsion and van der Waals attraction, augmented by microscopic details that include surface separation, water structure, ion hydration, and charge regulation at the interface, qualitatively reproduces the observed trends and implies that dispersion forces are responsible for establishing co-alignment in the solvent-separated state.

  13. Dissipative and electrostatic force spectroscopy of indium arsenide quantum dots by non-contact atomic force microscopy

    Science.gov (United States)

    Stomp, Romain-Pierre

    This thesis is devoted to the studies of self-assembled InAs quantum dots (QD) by low-temperature Atomic Force Microscopy (AFM) in frequency modulation mode. Several spectroscopic methods are developed to investigate single electron charging from a two-dimensional electron gas (2DEG) to an individual InAs QD. Furthermore, a new technique to measure the absolute tip-sample capacitance is also demonstrated. The main observables are the electrostatic force between the metal-coated AFM tip and sample as well as the sample-induced energy dissipation, and therefore no tunneling current has to be collected at the AFM tip. Measurements were performed by recording simultaneously the shift in the resonant frequency and the Q-factor degradation of the oscillating cantilever either as a function of tip-sample voltage or distance. The signature of single electron charging was detected as an abrupt change in the frequency shift as well as corresponding peaks in the dissipation. The main experimental features in the force agree well with the semi-classical theory of Coulomb blockade by considering the free energy of the system. The observed dissipation peaks can be understood as a back-action effect on the oscillating cantilever beam due to the fluctuation in time of electrons tunneling back and forth between the 2DEG and the QD. It was also possible to extract the absolute value of the tip-sample capacitance, as a consequence of the spectroscopic analysis of the electrostic force as a function of tip-sample distance for different values of the applied voltage. At the same time, the contact potential difference and the residual non-capacitive force could also be determined as a function of tip-sample distance.

  14. Computational Fluid Dynamics Modeling Three-Dimensional Unsteady Turbulent Flow and Excitation Force in Partial Admission Air Turbine

    Directory of Open Access Journals (Sweden)

    Yonghui Xie

    2013-01-01

    Full Text Available Air turbines are widely used to convert kinetic energy into power output in power engineering. The unsteady performance of air turbines with partial admission not only influences the aerodynamic performance and thermodynamic efficiency of turbine but also generates strong excitation force on blades to impair the turbine safely operating. Based on three-dimensional viscous compressible Navier-stokes equations, the present study employs RNG (Renormalization group k-ε turbulence model with finite volume discretization on air turbine with partial admission. Numerical models of four different admission rates with full annulus are built and analyzed via CFD (computational fluid dynamics modeling unsteady flows. Results indicate that the unsteady time-averaged isentropic efficiency is lower than the steady isentropic efficiency, and this difference rises as unsteady isentropic efficiency fluctuates stronger when the admission rate is reduced. The rotor axial and tangential forces with time are provided for all four admission rates. The low frequency excitation forces generated by partial admission are extraordinarily higher than the high frequency excitation