Modified atomic force microscope applied to the measurement of elastic modulus for a single peptide molecule

NASA Astrophysics Data System (ADS)

Ptak, Arkadiusz; Takeda, Seiji; Nakamura, Chikashi; Miyake, Jun; Kageshima, Masami; Jarvis, Suzanne P.; Tokumoto, Hiroshi

2001-09-01

A modified atomic force microscopy (AFM) system, based on a force modulation technique, has been used to find an approximate value for the elastic modulus of a single peptide molecule directly from a mechanical test. For this purpose a self-assembled monolayer built from two kinds of peptides, reactive (able to anchor to the AFM tip) and nonreactive, was synthesized. In a typical experiment a single C3K30C (C=cysteine, K=lysine) peptide molecule was stretched between a Au(111) substrate and the gold-coated tip of an AFM cantilever to which it was attached via gold-sulfur bonds. The amplitude of the cantilever oscillations, due to an external force applied via a magnetic particle to the cantilever, was recorded by a lock-in amplifier and recalculated into stiffness of the stretched molecule. A longitudinal Young's modulus for the α-helix of a single peptide molecule and for the elongated state of this molecule has been estimated. The obtained values; 1.2±0.3 and 50±15 GPa, for the peptide α-helix and elongated peptide backbone, respectively, seem to be reasonable comparing them to the Young's modulus of protein crystals and linear organic polymers. We believe this research opens up a means by which scientists can perform quantitative studies of the elastic properties of single molecule, especially of biologically important polymers like peptides or DNA.

The structure of [MnIII6 CrIII]3+ single-molecule magnets deposited in submono-layers and monolayers on surfaces studied by means of molecular resolved atomic force microscopy (AFM) and Kelvin Probe Force Microscopy in UHV

NASA Astrophysics Data System (ADS)

Heinzmann, U.; Gryzia, A.; Volkmann, T.; Brechling, A.; Hoeke, V.; Glaser, T.

2014-04-01

Single molecule magnets (SMM) deposited in submonolayers and monolayers have been analyzed with respect to their structures by means of non-contact AFM (topographic as well as damping mode) and Kelvin Probe Force Microscopy with molecular resolution.

Direct quantitative measurement of the C═O⋅⋅⋅H–C bond by atomic force microscopy

PubMed Central

Kawai, Shigeki; Nishiuchi, Tomohiko; Kodama, Takuya; Spijker, Peter; Pawlak, Rémy; Meier, Tobias; Tracey, John; Kubo, Takashi; Meyer, Ernst; Foster, Adam S.

2017-01-01

The hydrogen atom—the smallest and most abundant atom—is of utmost importance in physics and chemistry. Although many analysis methods have been applied to its study, direct observation of hydrogen atoms in a single molecule remains largely unexplored. We use atomic force microscopy (AFM) to resolve the outermost hydrogen atoms of propellane molecules via very weak C═O⋅⋅⋅H–C hydrogen bonding just before the onset of Pauli repulsion. The direct measurement of the interaction with a hydrogen atom paves the way for the identification of three-dimensional molecules such as DNAs and polymers, building the capabilities of AFM toward quantitative probing of local chemical reactivity. PMID:28508080

Reorganization energy upon charging a single molecule on an insulator measured by atomic force microscopy

NASA Astrophysics Data System (ADS)

Fatayer, Shadi; Schuler, Bruno; Steurer, Wolfram; Scivetti, Ivan; Repp, Jascha; Gross, Leo; Persson, Mats; Meyer, Gerhard

2018-05-01

Intermolecular single-electron transfer on electrically insulating films is a key process in molecular electronics1-4 and an important example of a redox reaction5,6. Electron-transfer rates in molecular systems depend on a few fundamental parameters, such as interadsorbate distance, temperature and, in particular, the Marcus reorganization energy7. This crucial parameter is the energy gain that results from the distortion of the equilibrium nuclear geometry in the molecule and its environment on charging8,9. The substrate, especially ionic films10, can have an important influence on the reorganization energy11,12. Reorganization energies are measured in electrochemistry13 as well as with optical14,15 and photoemission spectroscopies16,17, but not at the single-molecule limit and nor on insulating surfaces. Atomic force microscopy (AFM), with single-charge sensitivity18-22, atomic-scale spatial resolution20 and operable on insulating films, overcomes these challenges. Here, we investigate redox reactions of single naphthalocyanine (NPc) molecules on multilayered NaCl films. Employing the atomic force microscope as an ultralow current meter allows us to measure the differential conductance related to transitions between two charge states in both directions. Thereby, the reorganization energy of NPc on NaCl is determined as (0.8 ± 0.2) eV, and density functional theory (DFT) calculations provide the atomistic picture of the nuclear relaxations on charging. Our approach presents a route to perform tunnelling spectroscopy of single adsorbates on insulating substrates and provides insight into single-electron intermolecular transport.

Exploring the folding pattern of a polymer chain in a single crystal by combining single-molecule force spectroscopy and steered molecular dynamics simulations.

PubMed

Song, Yu; Feng, Wei; Liu, Kai; Yang, Peng; Zhang, Wenke; Zhang, Xi

2013-03-26

Understanding the folding pattern of a single polymer chain within its single crystal will shed light on the mechanism of crystallization. Here, we use the combined techniques of atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations to study the folding pattern of a polyethylene oxide (PEO) chain in its single crystal. Our results show that the folding pattern of a PEO chain in the crystal formed in dilute solution follows the adjacent re-entry folding model. While in the crystal obtained from the melt, the nonadjacent folding with large and irregular loops contributes to big force fluctuations in the force-extension curves. The method established here can offer a novel strategy to directly unravel the chain-folding pattern of polymer single crystals at single-molecule level.

Compressive Force Spectroscopy: From Living Cells to Single Proteins.

PubMed

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.

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

PubMed

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.

Nanotechnology Provides a New Perspective on Chemical Thermodynamics

ERIC Educational Resources Information Center

Haverkamp, Richard G.

2009-01-01

A small mechanical device, the atomic force microscope, measuring a force and the distance over which this force is applied, can be used on a single polysaccharide molecule to obtain the Gibbs energy of a conformational change within the polysaccharide. This well-defined conformational change within certain types of polysaccharide molecules is…

Principal Component Analysis of Lipid Molecule Conformational Changes in Molecular Dynamics Simulations.

PubMed

Buslaev, Pavel; Gordeliy, Valentin; Grudinin, Sergei; Gushchin, Ivan

2016-03-08

Molecular dynamics simulations of lipid bilayers are ubiquitous nowadays. Usually, either global properties of the bilayer or some particular characteristics of each lipid molecule are evaluated in such simulations, but the structural properties of the molecules as a whole are rarely studied. Here, we show how a comprehensive quantitative description of conformational space and dynamics of a single lipid molecule can be achieved via the principal component analysis (PCA). We illustrate the approach by analyzing and comparing simulations of DOPC bilayers obtained using eight different force fields: all-atom generalized AMBER, CHARMM27, CHARMM36, Lipid14, and Slipids and united-atom Berger, GROMOS43A1-S3, and GROMOS54A7. Similarly to proteins, most of the structural variance of a lipid molecule can be described by only a few principal components. These major components are similar in different simulations, although there are notable distinctions between the older and newer force fields and between the all-atom and united-atom force fields. The DOPC molecules in the simulations generally equilibrate on the time scales of tens to hundreds of nanoseconds. The equilibration is the slowest in the GAFF simulation and the fastest in the Slipids simulation. Somewhat unexpectedly, the equilibration in the united-atom force fields is generally slower than in the all-atom force fields. Overall, there is a clear separation between the more variable previous generation force fields and significantly more similar new generation force fields (CHARMM36, Lipid14, Slipids). We expect that the presented approaches will be useful for quantitative analysis of conformations and dynamics of individual lipid molecules in other simulations of lipid bilayers.

Nanomechanical DNA origami 'single-molecule beacons' directly imaged by atomic force microscopy

PubMed Central

Kuzuya, Akinori; Sakai, Yusuke; Yamazaki, Takahiro; Xu, Yan; Komiyama, Makoto

2011-01-01

DNA origami involves the folding of long single-stranded DNA into designed structures with the aid of short staple strands; such structures may enable the development of useful nanomechanical DNA devices. Here we develop versatile sensing systems for a variety of chemical and biological targets at molecular resolution. We have designed functional nanomechanical DNA origami devices that can be used as 'single-molecule beacons', and function as pinching devices. Using 'DNA origami pliers' and 'DNA origami forceps', which consist of two levers ~170 nm long connected at a fulcrum, various single-molecule inorganic and organic targets ranging from metal ions to proteins can be visually detected using atomic force microscopy by a shape transition of the origami devices. Any detection mechanism suitable for the target of interest, pinching, zipping or unzipping, can be chosen and used orthogonally with differently shaped origami devices in the same mixture using a single platform. PMID:21863016

Monovalent Strep-Tactin for strong and site-specific tethering in nanospectroscopy.

PubMed

Baumann, Fabian; Bauer, Magnus S; Milles, Lukas F; Alexandrovich, Alexander; Gaub, Hermann E; Pippig, Diana A

2016-01-01

Strep-Tactin, an engineered form of streptavidin, binds avidly to the genetically encoded peptide Strep-tag II in a manner comparable to streptavidin binding to biotin. These interactions have been used in protein purification and detection applications. However, in single-molecule studies, for example using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS), the tetravalency of these systems impedes the measurement of monodispersed data. Here, we introduce a monovalent form of Strep-Tactin that harbours a unique binding site for Strep-tag II and a single cysteine that allows Strep-Tactin to specifically attach to the atomic force microscope cantilever and form a consistent pulling geometry to obtain homogeneous rupture data. Using AFM-SMFS, the mechanical properties of the interaction between Strep-tag II and monovalent Strep-Tactin were characterized. Rupture forces comparable to biotin:streptavidin unbinding were observed. Using titin kinase and green fluorescent protein, we show that monovalent Strep-Tactin is generally applicable to protein unfolding experiments. We expect monovalent Strep-Tactin to be a reliable anchoring tool for a range of single-molecule studies.

Monovalent Strep-Tactin for strong and site-specific tethering in nanospectroscopy

NASA Astrophysics Data System (ADS)

Baumann, Fabian; Bauer, Magnus S.; Milles, Lukas F.; Alexandrovich, Alexander; Gaub, Hermann E.; Pippig, Diana A.

2016-01-01

Strep-Tactin, an engineered form of streptavidin, binds avidly to the genetically encoded peptide Strep-tag II in a manner comparable to streptavidin binding to biotin. These interactions have been used in protein purification and detection applications. However, in single-molecule studies, for example using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS), the tetravalency of these systems impedes the measurement of monodispersed data. Here, we introduce a monovalent form of Strep-Tactin that harbours a unique binding site for Strep-tag II and a single cysteine that allows Strep-Tactin to specifically attach to the atomic force microscope cantilever and form a consistent pulling geometry to obtain homogeneous rupture data. Using AFM-SMFS, the mechanical properties of the interaction between Strep-tag II and monovalent Strep-Tactin were characterized. Rupture forces comparable to biotin:streptavidin unbinding were observed. Using titin kinase and green fluorescent protein, we show that monovalent Strep-Tactin is generally applicable to protein unfolding experiments. We expect monovalent Strep-Tactin to be a reliable anchoring tool for a range of single-molecule studies.

Probe-based measurement of lateral single-electron transfer between individual molecules

PubMed Central

Steurer, Wolfram; Fatayer, Shadi; Gross, Leo; Meyer, Gerhard

2015-01-01

The field of molecular electronics aims at using single molecules as functional building blocks for electronics components, such as switches, rectifiers or transistors. A key challenge is to perform measurements with atomistic control over the alignment of the molecule and its contacting electrodes. Here we use atomic force microscopy to examine charge transfer between weakly coupled pentacene molecules on insulating films with single-electron sensitivity and control over the atomistic details. We show that, in addition to the imaging capability, the probe tip can be used to control the charge state of individual molecules and to detect charge transfers to/from the tip, as well as between individual molecules. Our approach represents a novel route for molecular charge transfer studies with a host of opportunities, especially in combination with single atom/molecule manipulation and nanopatterning techniques. PMID:26387533

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

PubMed

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.

Synthesis And Single Molecule Force Spectroscopy Of Poly(hydroxyethyl methacrylate-g-ethylene glycol)

NASA Astrophysics Data System (ADS)

Zhang, Dong; Ortiz, Christine

2003-03-01

With the advent of nanotechnology, miniaturized devices will soon need nanoscale springs with well-controlled nanomechanical properties such as shock absorbers, or to control the adhesive interactions between two components. In order to understand, manipulate, and control single macromolecule nanomechanical properties, mono(thiol)-terminated poly(hydroxyethyl methacrylate-g-ethylene glycol) has been synthesized via atom transfer radical polymerization. End-functionalization, chemical structure, molecular weight, side-chain graft density, radius of gyration, and polydispersity were characterized by 1H nuclear magnetic resonance, static light scattering, and gel permeation chromatography. The polymer chains were attached to Au-coated Si wafers via chemisorption to prepare well-separated "mushrooms", as verified by atomic force microscopy. Single molecule force spectroscopy was then used to measure the extensional elastic properties, i.e. force (nN) versus end-to-end separation distance (nm), of the individual chains by tethering to a Si3N4 probe tip via nonspecific, physisorption interactions.

Non-additivity of molecule-surface van der Waals potentials from force measurements.

PubMed

Wagner, Christian; Fournier, Norman; Ruiz, Victor G; Li, Chen; Müllen, Klaus; Rohlfing, Michael; Tkatchenko, Alexandre; Temirov, Ruslan; Tautz, F Stefan

2014-11-26

Van der Waals (vdW) forces act ubiquitously in condensed matter. Despite being weak on an atomic level, they substantially influence molecular and biological systems due to their long range and system-size scaling. The difficulty to isolate and measure vdW forces on a single-molecule level causes our present understanding to be strongly theory based. Here we show measurements of the attractive potential between differently sized organic molecules and a metal surface using an atomic force microscope. Our choice of molecules and the large molecule-surface separation cause this attraction to be purely of vdW type. The experiment allows testing the asymptotic vdW force law and its validity range. We find a superlinear growth of the vdW attraction with molecular size, originating from the increased deconfinement of electrons in the molecules. Because such non-additive vdW contributions are not accounted for in most first-principles or empirical calculations, we suggest further development in that direction.

Diffuse X-ray scattering from benzil, C(14)H(10)O(2): analysis via automatic refinement of a Monte Carlo model.

PubMed

Welberry, T R; Goossens, D J; Edwards, A J; David, W I

2001-01-01

A recently developed method for fitting a Monte Carlo computer-simulation model to observed single-crystal diffuse X-ray scattering has been used to study the diffuse scattering in benzil, diphenylethanedione, C(6)H(5)-CO-CO-C(6)H(5). A model involving 13 parameters consisting of 11 intermolecular force constants, a single intramolecular torsional force constant and a local Debye-Waller factor was refined to give an agreement factor, R = [summation operator omega(Delta I)(2)/summation operator omega I(obs)(2)](1/2), of 14.5% for 101,324 data points. The model was purely thermal in nature. The analysis has shown that the diffuse lines, which feature so prominently in the observed diffraction patterns, are due to strong longitudinal displacement correlations. These are transmitted from molecule to molecule via a network of contacts involving hydrogen bonding of an O atom on one molecule and the para H atom of the phenyl ring of a neighbouring molecule. The analysis also allowed the determination of a torsional force constant for rotations about the single bonds in the molecule. This is the first diffuse scattering study in which measurement of such internal molecular torsion forces has been attempted.

Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, Using Single Molecule Atomic Force Spectroscopy.

PubMed

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.

Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, Using Single Molecule Atomic Force Spectroscopy

PubMed Central

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. PMID:27183010

Characterization of novel sufraces by FTIR spectroscopy and atomic force microscopy for food pathogen detection

USDA-ARS?s Scientific Manuscript database

Single molecular detection of pathogens and toxins of interest to food safety is within grasp using technology such as Atomic Force Microscopy. Using antibodies or specific aptamers connected to the AFM tip make it possible to detect a pathogen molecule on a surface. However, it also becomes necess...

Measuring the mechanical properties of molecular conformers

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

Force and Conductance Spectroscopy of Single Molecule Junctions

NASA Astrophysics Data System (ADS)

Frei, Michael

Investigation of mechanical properties of single molecule junctions is crucial to develop an understanding and enable control of single molecular junctions. This work presents an experimental and analytical approach that enables the statistical evaluation of force and simultaneous conductance data of metallic atomic point contacts and molecular junctions. A conductive atomic force microscope based break junction technique is developed to form single molecular junctions and collect conductance and force data simultaneously. Improvements of the optical components have been achieved through the use of a super-luminescent diode, enabling tremendous increases in force resolution. An experimental procedure to collect data for various molecular junctions has been developed and includes deposition, calibration, and analysis methods. For the statistical analysis of force, novel approaches based on two dimensional histograms and a direct force identification method are presented. The two dimensional method allows for an unbiased evaluation of force events that are identified using corresponding conductance signatures. This is not always possible however, and in these situations, the force based identification of junction rearrangement events is an attractive alternative method. This combined experimental and analytical approach is then applied to three studies: First, the impact of molecular backbones to the mechanical behavior of single molecule junctions is investigated and it is found that junctions formed with identical linkers but different backbone structure result in junctions with varying breaking forces. All molecules used show a clear molecular signature and force data can be evaluated using the 2D method. Second, the effects of the linker group used to attach molecules to gold electrodes are investigated. A study of four alkane molecules with different linkers finds a drastic difference in the evolution of donor-acceptor and covalently bonded molecules respectively. In fact, the covalent bond is found to significantly distort the metal electrode rearrangement such that junction rearrangement events can no longer be identified with a clean and well defined conductance signature. For this case, the force based identification process is used. Third, results for break junction measurements with different metals are presented. It is found that silver and palladium junctions rupture with forces different from those of gold contacts. In the case of silver experiments in ambient conditions, we can also identify oxygen impurities in the silver contact formation process, leading to force and conductance measurements of silver-oxygen structures. For the future, this work provides an experimental and analytical foundation that will enable insights into single molecule systems not previously accessible.

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

NASA Astrophysics Data System (ADS)

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

2007-01-01

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

Atomic force microscope observation of branching in single transcript molecules derived from human cardiac muscle

NASA Astrophysics Data System (ADS)

Reed, Jason; Hsueh, Carlin; Mishra, Bud; Gimzewski, James K.

2008-09-01

We have used an atomic force microscope to examine a clinically derived sample of single-molecule gene transcripts, in the form of double-stranded cDNA, (c: complementary) obtained from human cardiac muscle without the use of polymerase chain reaction (PCR) amplification. We observed a log-normal distribution of transcript sizes, with most molecules being in the range of 0.4-7.0 kilobase pairs (kb) or 130-2300 nm in contour length, in accordance with the expected distribution of mRNA (m: messenger) sizes in mammalian cells. We observed novel branching structures not previously known to exist in cDNA, and which could have profound negative effects on traditional analysis of cDNA samples through cloning, PCR and DNA sequencing.

Surface conformations of anti-ricin aptamer and its affinity to ricin determined by atomic force microscopy and surface plasmon resonance

USDA-ARS?s Scientific Manuscript database

The specific interactions between ricin and anti-ricin aptamer were measured with atomic force microscopy (AFM) and surface plasmon resonance (SPR) spectrometry and the results were compared. In AFM, a single-molecule experiment with ricin functionalized AFM tip was used for scanning the aptamer mol...

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

PubMed

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.

β-connectin studies by small-angle x-ray scattering and single-molecule force spectroscopy by atomic force microscopy

NASA Astrophysics Data System (ADS)

Marchetti, S.; Sbrana, F.; Toscano, A.; Fratini, E.; Carlà, M.; Vassalli, M.; Tiribilli, B.; Pacini, A.; Gambi, C. M. C.

2011-05-01

The three-dimensional structure and the mechanical properties of a β-connectin fragment from human cardiac muscle, belonging to the I band, from I27 to I34, were investigated by small-angle x-ray scattering (SAXS) and single-molecule force spectroscopy (SMFS). This molecule presents an entropic elasticity behavior, associated to globular domain unfolding, that has been widely studied in the last 10 years. In addition, atomic force microscopy based SMFS experiments suggest that this molecule has an additional elastic regime, for low forces, probably associated to tertiary structure remodeling. From a structural point of view, this behavior is a mark of the fact that the eight domains in the I27-I34 fragment are not independent and they organize in solution, assuming a well-defined three-dimensional structure. This hypothesis has been confirmed by SAXS scattering, both on a diluted and a concentrated sample. Two different models were used to fit the SAXS curves: one assuming a globular shape and one corresponding to an elongated conformation, both coupled with a Coulomb repulsion potential to take into account the protein-protein interaction. Due to the predominance of the structure factor, the effective shape of the protein in solution could not be clearly disclosed. By performing SMFS by atomic force microscopy, mechanical unfolding properties were investigated. Typical sawtooth profiles were obtained and the rupture force of each unfolding domain was estimated. By fitting a wormlike chain model to each peak of the sawtooth profile, the entropic elasticity of octamer was described.

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

PubMed

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

2018-06-01

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

Electrons, Photons, and Force: Quantitative Single-Molecule Measurements from Physics to Biology

PubMed Central

2011-01-01

Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution. PMID:21338175

Fabricating Atom-Sized Gaps by Field-Aided Atom Migration in Nanoscale Junctions

NASA Astrophysics Data System (ADS)

Liu, Ran; Bi, Jun-Jie; Xie, Zhen; Yin, Kaikai; Wang, Dunyou; Zhang, Guang-Ping; Xiang, Dong; Wang, Chuan-Kui; Li, Zong-Liang

2018-05-01

The gap sizes between electrodes generated by typical methods are generally much larger than the dimension of a common molecule when fabricating a single-molecule junction, which dramatically suppresses the yield of single-molecule junctions. Based on the ab initio calculations, we develop a strategy named the field-aided method to accurately fabricate an atomic-sized gap between gold nanoelectrodes. To understand the mechanism of this strategy, configuration evolutions of gold nanojunction in stretching and compressing processes are calculated. The numerical results show that, in the stretching process, the gold atoms bridged between two electrodes are likely to form atomic chains. More significantly, lattice vacant positions can be easily generated in stretching and compressing processes, which make field-aided gap generation possible. In field-aided atom migration (FAAM), the external field can exert driving force, enhance the initial energy of the system, and decrease the barrier in the migration path, which makes the atom migration feasible. Conductance and stretching and compressing forces, as measurable variables in stretching and compressing processes, present very useful signals for determining the time to perform FAAM. Following this desirable strategy, we successfully fabricate gold nanogaps with a dimension of 0.38 ±0.05 nm in the experiment, as our calculation simulates.

Mechanical design of proteins studied by single-molecule force spectroscopy and protein engineering.

PubMed

Carrion-Vazquez, M; Oberhauser, A F; Fisher, T E; Marszalek, P E; Li, H; Fernandez, J M

2000-01-01

Mechanical unfolding and refolding may regulate the molecular elasticity of modular proteins with mechanical functions. The development of the atomic force microscopy (AFM) has recently enabled the dynamic measurement of these processes at the single-molecule level. Protein engineering techniques allow the construction of homomeric polyproteins for the precise analysis of the mechanical unfolding of single domains. alpha-Helical domains are mechanically compliant, whereas beta-sandwich domains, particularly those that resist unfolding with backbone hydrogen bonds between strands perpendicular to the applied force, are more stable and appear frequently in proteins subject to mechanical forces. The mechanical stability of a domain seems to be determined by its hydrogen bonding pattern and is correlated with its kinetic stability rather than its thermodynamic stability. Force spectroscopy using AFM promises to elucidate the dynamic mechanical properties of a wide variety of proteins at the single molecule level and provide an important complement to other structural and dynamic techniques (e.g., X-ray crystallography, NMR spectroscopy, patch-clamp).

Following aptamer-ricin specific binding by single molecule recognition and force spectroscopy measurements

USDA-ARS?s Scientific Manuscript database

The atomic force microscope (AFM) recognition and dynamic force spectroscopy (DFS) experiments provide both morphology and interaction information of the aptamer and protein, which can be used for the future study on the thermodynamics and kinetics properties of ricin-aptamer/antibody interactions. ...

[Atomic force microscopy: a tool to analyze the viral cycle].

PubMed

Bernaud, Julien; Castelnovo, Martin; Muriaux, Delphine; Faivre-Moskalenko, Cendrine

2015-05-01

Each step of the HIV-1 life cycle frequently involves a change in the morphology and/or mechanical properties of the viral particle or core. The atomic force microscope (AFM) constitutes a powerful tool for characterizing these physical changes at the scale of a single virus. Indeed, AFM enables the visualization of viral capsids in a controlled physiological environment and to probe their mechanical properties by nano-indentation. Finally, AFM force spectroscopy allows to characterize the affinities between viral envelope proteins and cell receptors at the single molecule level. © 2015 médecine/sciences – Inserm.

Influence of atomic tip structure on the intensity of inelastic tunneling spectroscopy data analyzed by combined scanning tunneling spectroscopy, force microscopy, and density functional theory

NASA Astrophysics Data System (ADS)

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

2016-04-01

Achieving a high intensity in inelastic scanning tunneling spectroscopy (IETS) is important for precise measurements. The intensity of the IETS signal can vary by up to a factor of 3 for various tips without an apparent reason accessible by scanning tunneling microscopy (STM) alone. Here, we show that combining STM and IETS with atomic force microscopy enables carbon monoxide front-atom identification, revealing that high IETS intensities for CO/Cu(111) are obtained for single-atom tips, while the intensity drops sharply for multiatom tips. Adsorption of the CO molecule on a Cu adatom [CO/Cu/Cu(111)] such that the molecule is elevated over the substrate strongly diminishes the tip dependence of IETS intensity, showing that an elevated position channels most of the tunneling current through the CO molecule even for multiatom tips, while a large fraction of the tunneling current bypasses the CO molecule in the case of CO/Cu(111).

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

NASA Astrophysics Data System (ADS)

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

2013-05-01

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

Direct, concurrent measurements of the forces and currents affecting DNA in a nanopore with comparable topography.

PubMed

Nelson, Edward M; Li, Hui; Timp, Gregory

2014-06-24

We report direct, concurrent measurements of the forces and currents associated with the translocation of a single-stranded DNA molecule tethered to the tip of an atomic force microscope (AFM) cantilever through synthetic pores with topagraphies comparable to the DNA. These measurements were performed to gauge the signal available for sequencing and the electric force required to impel a single molecule through synthetic nanopores ranging from 1.0 to 3.5 nm in diameter in silicon nitride membranes 6-10 nm thick. The measurements revealed that a molecule can slide relatively frictionlessly through a pore, but regular fluctuations are observed intermittently in the force (and the current) every 0.35-0.72 nm, which are attributed to individual nucleotides translating through the nanopore in a turnstile-like motion.

Electrical Conductivity of Ferritin Proteins by Conductive AFM

NASA Technical Reports Server (NTRS)

Xu, Degao; Watt, Gerald D.; Harb, John N.; Davis, Robert C.

2005-01-01

Electrical conductivity measurements were performed on single apoferritin and holoferritin molecules by conductive atomic force microscopy. Conductivity of self-assembled monolayer films of ferritin molecules on gold surfaces was also measured. Holoferritin was 5-25 times more conductive than apoferritin, indicating that for holoferritin most electron-transfer goes through the ferrihydrite core. With 1 V applied, the average electrical currents through single holoferritin and apoferritin molecules were 2.6 PA and 0.19 PA, respectively.

Specificity and mechanism of action of alpha-helical membrane-active peptides interacting with model and biological membranes by single-molecule force spectroscopy.

PubMed

Sun, Shiyu; Zhao, Guangxu; Huang, Yibing; Cai, Mingjun; Shan, Yuping; Wang, Hongda; Chen, Yuxin

2016-07-01

In this study, to systematically investigate the targeting specificity of membrane-active peptides on different types of cell membranes, we evaluated the effects of peptides on different large unilamellar vesicles mimicking prokaryotic, normal eukaryotic, and cancer cell membranes by single-molecule force spectroscopy and spectrum technology. We revealed that cationic membrane-active peptides can exclusively target negatively charged prokaryotic and cancer cell model membranes rather than normal eukaryotic cell model membranes. Using Acholeplasma laidlawii, 3T3-L1, and HeLa cells to represent prokaryotic cells, normal eukaryotic cells, and cancer cells in atomic force microscopy experiments, respectively, we further studied that the single-molecule targeting interaction between peptides and biological membranes. Antimicrobial and anticancer activities of peptides exhibited strong correlations with the interaction probability determined by single-molecule force spectroscopy, which illustrates strong correlations of peptide biological activities and peptide hydrophobicity and charge. Peptide specificity significantly depends on the lipid compositions of different cell membranes, which validates the de novo design of peptide therapeutics against bacteria and cancers.

Modeling single molecule junction mechanics as a probe of interface bonding

NASA Astrophysics Data System (ADS)

Hybertsen, Mark S.

2017-03-01

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. A set of exemplary model junction structures has been analyzed using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond to the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N-Au and S-Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. The results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.

Modeling single molecule junction mechanics as a probe of interface bonding

DOE PAGES

Hybertsen, Mark S.

2017-03-07

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. We analyzed a set of exemplary model junction structures using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond tomore » the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N–Au and S–Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This, then, allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. Our results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.« less

Modeling single molecule junction mechanics as a probe of interface bonding

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

Hybertsen, Mark S.

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. We analyzed a set of exemplary model junction structures using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond tomore » the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N–Au and S–Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This, then, allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. Our results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.« less

Monodisperse measurement of the biotin-streptavidin interaction strength in a well-defined pulling geometry

PubMed Central

Sedlak, Steffen M.; Bauer, Magnus S.; Kluger, Carleen; Schendel, Leonard C.; Milles, Lukas F.; Pippig, Diana A.

2017-01-01

The widely used interaction of the homotetramer streptavidin with the small molecule biotin has been intensively studied by force spectroscopy and has become a model system for receptor ligand interaction. However, streptavidin’s tetravalency results in diverse force propagation pathways through the different binding interfaces. This multiplicity gives rise to polydisperse force spectroscopy data. Here, we present an engineered monovalent streptavidin tetramer with a single cysteine in its functional subunit that allows for site-specific immobilization of the molecule, orthogonal to biotin binding. Functionality of streptavidin and its binding properties for biotin remain unaffected. We thus created a stable and reliable molecular anchor with a unique high-affinity binding site for biotinylated molecules or nanoparticles, which we expect to be useful for many single-molecule applications. To characterize the mechanical properties of the bond between biotin and our monovalent streptavidin, we performed force spectroscopy experiments using an atomic force microscope. We were able to conduct measurements at the single-molecule level with 1:1-stoichiometry and a well-defined geometry, in which force exclusively propagates through a single subunit of the streptavidin tetramer. For different force loading rates, we obtained narrow force distributions of the bond rupture forces ranging from 200 pN at 1,500 pN/s to 230 pN at 110,000 pN/s. The data are in very good agreement with the standard Bell-Evans model with a single potential barrier at Δx0 = 0.38 nm and a zero-force off-rate koff,0 in the 10−6 s-1 range. PMID:29206886

Monodisperse measurement of the biotin-streptavidin interaction strength in a well-defined pulling geometry.

PubMed

Sedlak, Steffen M; Bauer, Magnus S; Kluger, Carleen; Schendel, Leonard C; Milles, Lukas F; Pippig, Diana A; Gaub, Hermann E

2017-01-01

The widely used interaction of the homotetramer streptavidin with the small molecule biotin has been intensively studied by force spectroscopy and has become a model system for receptor ligand interaction. However, streptavidin's tetravalency results in diverse force propagation pathways through the different binding interfaces. This multiplicity gives rise to polydisperse force spectroscopy data. Here, we present an engineered monovalent streptavidin tetramer with a single cysteine in its functional subunit that allows for site-specific immobilization of the molecule, orthogonal to biotin binding. Functionality of streptavidin and its binding properties for biotin remain unaffected. We thus created a stable and reliable molecular anchor with a unique high-affinity binding site for biotinylated molecules or nanoparticles, which we expect to be useful for many single-molecule applications. To characterize the mechanical properties of the bond between biotin and our monovalent streptavidin, we performed force spectroscopy experiments using an atomic force microscope. We were able to conduct measurements at the single-molecule level with 1:1-stoichiometry and a well-defined geometry, in which force exclusively propagates through a single subunit of the streptavidin tetramer. For different force loading rates, we obtained narrow force distributions of the bond rupture forces ranging from 200 pN at 1,500 pN/s to 230 pN at 110,000 pN/s. The data are in very good agreement with the standard Bell-Evans model with a single potential barrier at Δx0 = 0.38 nm and a zero-force off-rate koff,0 in the 10-6 s-1 range.

Forces in yeast flocculation

NASA Astrophysics Data System (ADS)

El-Kirat-Chatel, Sofiane; Beaussart, Audrey; Vincent, Stéphane P.; Abellán Flos, Marta; Hols, Pascal; Lipke, Peter N.; Dufrêne, Yves F.

2015-01-01

In the baker's yeast Saccharomyces cerevisiae, cell-cell adhesion (``flocculation'') is conferred by a family of lectin-like proteins known as the flocculin (Flo) proteins. Knowledge of the adhesive and mechanical properties of flocculins is important for understanding the mechanisms of yeast adhesion, and may help controlling yeast behaviour in biotechnology. We use single-molecule and single-cell atomic force microscopy (AFM) to explore the nanoscale forces engaged in yeast flocculation, focusing on the role of Flo1 as a prototype of flocculins. Using AFM tips labelled with mannose, we detect single flocculins on Flo1-expressing cells, showing they are widely exposed on the cell surface. When subjected to force, individual Flo1 proteins display two distinct force responses, i.e. weak lectin binding forces and strong unfolding forces reflecting the force-induced extension of hydrophobic tandem repeats. We demonstrate that cell-cell adhesion bonds also involve multiple weak lectin interactions together with strong unfolding forces, both associated with Flo1 molecules. Single-molecule and single-cell data correlate with microscale cell adhesion behaviour, suggesting strongly that Flo1 mechanics is critical for yeast flocculation. These results favour a model in which not only weak lectin-sugar interactions are involved in yeast flocculation but also strong hydrophobic interactions resulting from protein unfolding.

Simple Model for the Benzene Hexafluorobenzene Interaction

DOE PAGES

Tillack, Andreas F.; Robinson, Bruce H.

2017-06-05

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

Simple Model for the Benzene Hexafluorobenzene Interaction

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

Tillack, Andreas F.; Robinson, Bruce H.

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

Direct Force Measurements of Receptor-Ligand Interactions on Living Cells

NASA Astrophysics Data System (ADS)

Eibl, Robert H.

The characterization of cell adhesion between two living cells at the level of single receptor-ligand bonds is an experimental challenge. This chapter describes how the extremely sensitive method of atomic force microscopy (AFM) based force spectroscopy can be applied to living cells in order to probe for cell-to-cell or cell-to-substrate interactions mediated by single pairs of adhesion receptors. In addition, it is outlined how single-molecule AFM force spectroscopy can be used to detect physiologic changes of an adhesion receptor in a living cell. This force spectroscopy allows us to detect in living cells rapidly changing, chemokine SDF-1 triggered activation states of single VLA-4 receptors. This recently developed AFM application will allow for the detailed investigation of the integrin-chemokine crosstalk of integrin activation mechanisms and on how other adhesion receptors are modulated in health and disease. As adhesion molecules, living cells and even bacteria can be studied by single-molecule AFM force spectroscopy, this method is set to become a powerful tool that can not only be used in biophysics, but in cell biology as well as in immunology and cancer research.

Evaluation of synthetic linear motor-molecule actuation energetics

PubMed Central

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

2006-01-01

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

Single-molecule Force Spectroscopy Approach to Enzyme Catalysis*

PubMed Central

Alegre-Cebollada, Jorge; Perez-Jimenez, Raul; Kosuri, Pallav; Fernandez, Julio M.

2010-01-01

Enzyme catalysis has been traditionally studied using a diverse set of techniques such as bulk biochemistry, x-ray crystallography, and NMR. Recently, single-molecule force spectroscopy by atomic force microscopy has been used as a new tool to study the catalytic properties of an enzyme. In this approach, a mechanical force ranging up to hundreds of piconewtons is applied to the substrate of an enzymatic reaction, altering the conformational energy of the substrate-enzyme interactions during catalysis. From these measurements, the force dependence of an enzymatic reaction can be determined. The force dependence provides valuable new information about the dynamics of enzyme catalysis with sub-angstrom resolution, a feat unmatched by any other current technique. To date, single-molecule force spectroscopy has been applied to gain insight into the reduction of disulfide bonds by different enzymes of the thioredoxin family. This minireview aims to present a perspective on this new approach to study enzyme catalysis and to summarize the results that have already been obtained from it. Finally, the specific requirements that must be fulfilled to apply this new methodology to any other enzyme will be discussed. PMID:20382731

Single-molecule force spectroscopy approach to enzyme catalysis.

PubMed

Alegre-Cebollada, Jorge; Perez-Jimenez, Raul; Kosuri, Pallav; Fernandez, Julio M

2010-06-18

Enzyme catalysis has been traditionally studied using a diverse set of techniques such as bulk biochemistry, x-ray crystallography, and NMR. Recently, single-molecule force spectroscopy by atomic force microscopy has been used as a new tool to study the catalytic properties of an enzyme. In this approach, a mechanical force ranging up to hundreds of piconewtons is applied to the substrate of an enzymatic reaction, altering the conformational energy of the substrate-enzyme interactions during catalysis. From these measurements, the force dependence of an enzymatic reaction can be determined. The force dependence provides valuable new information about the dynamics of enzyme catalysis with sub-angstrom resolution, a feat unmatched by any other current technique. To date, single-molecule force spectroscopy has been applied to gain insight into the reduction of disulfide bonds by different enzymes of the thioredoxin family. This minireview aims to present a perspective on this new approach to study enzyme catalysis and to summarize the results that have already been obtained from it. Finally, the specific requirements that must be fulfilled to apply this new methodology to any other enzyme will be discussed.

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

PubMed Central

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

2014-01-01

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

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

PubMed

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.

Reducing uncertainties in energy dissipation measurements in atomic force spectroscopy of molecular networks and cell-adhesion studies.

PubMed

Biswas, Soma; Leitao, Samuel; Theillaud, Quentin; Erickson, Blake W; Fantner, Georg E

2018-06-20

Atomic force microscope (AFM) based single molecule force spectroscopy (SMFS) is a valuable tool in biophysics to investigate the ligand-receptor interactions, cell adhesion and cell mechanics. However, the force spectroscopy data analysis needs to be done carefully to extract the required quantitative parameters correctly. Especially the large number of molecules, commonly involved in complex networks formation; leads to very complicated force spectroscopy curves. One therefore, generally characterizes the total dissipated energy over a whole pulling cycle, as it is difficult to decompose the complex force curves into individual single molecule events. However, calculating the energy dissipation directly from the transformed force spectroscopy curves can lead to a significant over-estimation of the dissipated energy during a pulling experiment. The over-estimation of dissipated energy arises from the finite stiffness of the cantilever used for AFM based SMFS. Although this error can be significant, it is generally not compensated for. This can lead to significant misinterpretation of the energy dissipation (up to the order of 30%). In this paper, we show how in complex SMFS the excess dissipated energy caused by the stiffness of the cantilever can be identified and corrected using a high throughput algorithm. This algorithm is then applied to experimental results from molecular networks and cell-adhesion measurements to quantify the improvement in the estimation of the total energy dissipation.

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

PubMed

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.

Submolecular resolution in scanning probe images of Sn-phthalocyanines on Cu(1 0 0) using metal tips

NASA Astrophysics Data System (ADS)

Buchmann, Kristof; Hauptmann, Nadine; Foster, Adam S.; Berndt, Richard

2017-10-01

Single Sn-phthalocyanine (SnPc) molecules adsorb on Cu(1 0 0) with the Sn ion above (Sn-up) or below (Sn-down) the molecular plane. Here we use a combination of atomic force microscopy (AFM), scanning tunnelling microscopy (STM) and first principles calculations to understand the adsorption configuration and origin of observed contrast of molecules in the Sn-down state. AFM with metallic tips images the pyrrole nitrogen atoms in these molecules as attractive features while STM reveals a chirality of the electronic structure of the molecules close to the Fermi level E_F, which is not observed in AFM. Using density functional theory calculations, the origin of the submolecular contrast is analysed and, while the electrostatic forces turn out to be negligible, the van der Waals interaction between the phenyl rings of SnPc and the substrate deform the molecule, push the pyrrole nitrogen atoms away from the substrate and thus induce the observed submolecular contrast. Simulated STM images reproduce the chirality of the electronic structure near E_F.

Set-up of a high-resolution 300 mK atomic force microscope in an ultra-high vacuum compatible (3)He/10 T cryostat.

PubMed

von Allwörden, H; Ruschmeier, K; Köhler, A; Eelbo, T; Schwarz, A; Wiesendanger, R

2016-07-01

The design of an atomic force microscope with an all-fiber interferometric detection scheme capable of atomic resolution at about 500 mK is presented. The microscope body is connected to a small pumped (3)He reservoir with a base temperature of about 300 mK. The bakeable insert with the cooling stage can be moved from its measurement position inside the bore of a superconducting 10 T magnet into an ultra-high vacuum chamber, where the tip and sample can be exchanged in situ. Moreover, single atoms or molecules can be evaporated onto a cold substrate located inside the microscope. Two side chambers are equipped with standard surface preparation and surface analysis tools. The performance of the microscope at low temperatures is demonstrated by resolving single Co atoms on Mn/W(110) and by showing atomic resolution on NaCl(001).

Single-Molecule Tribology: Force Microscopy Manipulation of a Porphyrin Derivative on a Copper Surface.

PubMed

Pawlak, Rémy; Ouyang, Wengen; Filippov, Alexander E; Kalikhman-Razvozov, Lena; Kawai, Shigeki; Glatzel, Thilo; Gnecco, Enrico; Baratoff, Alexis; Zheng, Quanshui; Hod, Oded; Urbakh, Michael; Meyer, Ernst

2016-01-26

The low-temperature mechanical response of a single porphyrin molecule attached to the apex of an atomic force microscope (AFM) tip during vertical and lateral manipulations is studied. We find that approach-retraction cycles as well as surface scanning with the terminated tip result in atomic-scale friction patterns induced by the internal reorientations of the molecule. With a joint experimental and computational effort, we identify the dicyanophenyl side groups of the molecule interacting with the surface as the dominant factor determining the observed frictional behavior. To this end, we developed a generalized Prandtl-Tomlinson model parametrized using density functional theory calculations that includes the internal degrees of freedom of the side group with respect to the core and its interactions with the underlying surface. We demonstrate that the friction pattern results from the variations of the bond length and bond angles between the dicyanophenyl side group and the porphyrin backbone as well as those of the CN group facing the surface during the lateral and vertical motion of the AFM tip.

Single molecule atomic force microscopy and force spectroscopy of chitosan.

PubMed

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.

Advances in single-molecule magnet surface patterning through microcontact printing.

PubMed

Mannini, Matteo; Bonacchi, Daniele; Zobbi, Laura; Piras, Federica M; Speets, Emiel A; Caneschi, Andrea; Cornia, Andrea; Magnani, Agnese; Ravoo, Bart Jan; Reinhoudt, David N; Sessoli, Roberta; Gatteschi, Dante

2005-07-01

We present an implementation of strategies to deposit single-molecule magnets (SMMs) using microcontact printing microCP). We describe different approaches of microCP to print stripes of a sulfur-functionalized dodecamanganese (III, IV) cluster on gold surfaces. Comparison by atomic force microscopy profile analysis of the patterned structures confirms the formation of a chemically stable single layer of SMMs. Images based on chemical contrast, obtained by time-of-flight secondary ion mass spectrometry, confirm the patterned structure.

Analysis of DNA interactions using single-molecule force spectroscopy.

PubMed

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.

Preparation and single molecule structure of electroactive polysilane end-grafted on a crystalline silicon surface

NASA Astrophysics Data System (ADS)

Furukawa, Kazuaki; Ebata, Keisuke

2000-12-01

Electrically active polysilanes of poly(methylphenylsilane) (PMPS) and poly[bis(p-n-butylphenyl)silane] (PBPS), which are, respectively, known as a good hole transporting material and a near-ultraviolet electroluminescent material, are end-grafted directly on a crystalline silicon surface. The single polysilane molecules are clearly distinguished one from the other on the surface by means of atomic force microscopy observations. End-grafted single molecules of PMPS are observed as dots while end-grafted PBPS appear as worms extending for more than 100 nm on the crystalline silicon surface.

The Chemical Structure and Acid Deterioration of Paper.

ERIC Educational Resources Information Center

Hollinger, William K., Jr.

1984-01-01

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

Packaging of single DNA molecules by the yeast mitochondrial protein Abf2p.

PubMed

Brewer, Laurence R; Friddle, Raymond; Noy, Aleksandr; Baldwin, Enoch; Martin, Shelley S; Corzett, Michele; Balhorn, Rod; Baskin, Ronald J

2003-10-01

Mitochondrial and nuclear DNA are packaged by proteins in a very different manner. Although protein-DNA complexes called "nucleoids" have been identified as the genetic units of mitochondrial inheritance in yeast and man, little is known about their physical structure. The yeast mitochondrial protein Abf2p was shown to be sufficient to compact linear dsDNA, without the benefit of supercoiling, using optical and atomic force microscopy single molecule techniques. The packaging of DNA by Abf2p was observed to be very weak as evidenced by a fast Abf2p off-rate (k(off) = 0.014 +/- 0.001 s(-1)) and the extremely small forces (<0.6 pN) stabilizing the condensed protein-DNA complex. Atomic force microscopy images of individual complexes showed the 190-nm structures are loosely packaged relative to nuclear chromatin. This organization may leave mtDNA accessible for transcription and replication, while making it more vulnerable to damage.

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

PubMed Central

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

2010-01-01

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

Covalent bond force profile and cleavage in a single polymer chain

NASA Astrophysics Data System (ADS)

Garnier, Lionel; Gauthier-Manuel, Bernard; van der Vegte, Eric W.; Snijders, Jaap; Hadziioannou, Georges

2000-08-01

We present here the measurement of the single-polymer entropic elasticity and the single covalent bond force profile, probed with two types of atomic force microscopes (AFM) on a synthetic polymer molecule: polymethacrylic acid in water. The conventional AFM allowed us to distinguish two types of interactions present in this system when doing force spectroscopic measurements: the first interaction is associated with adsorption sites of the polymer chains onto a bare gold surface, the second interaction is directly correlated to the rupture process of a single covalent bond. All these bridging interactions allowed us to stretch the single polymer chain and to determine the various factors playing a role in the elasticity of these molecules. To obtain a closer insight into the bond rupture process, we moved to a force sensor stable in position when measuring attractive forces. By optimizing the polymer length so as to fulfill the elastic stability conditions, we were able for the first time to map out the entire force profile associated with the cleavage of a single covalent bond. Experimental data coupled with molecular quantum mechanical calculations strongly suggest that the breaking bond is located at one end of the polymer chain.

Analysis of acid-base interactions at Al2O3 (11-20) interfaces by means of single molecule force spectroscopy

NASA Astrophysics Data System (ADS)

Mosebach, Bastian; Ozkaya, Berkem; Giner, Ignacio; Keller, Adrian; Grundmeier, Guido

2017-10-01

Single molecule force spectroscopy (SMFS) was employed to investigate the interaction forces between aliphatic amino, hydroxyl and ether groups and aluminum oxide single crystal surfaces in an aqueous electrolyte at pH = 6. The force studies were based on the variation of the terminal group of polyethylene glycol which was bound via a Ssbnd Au bond to the gold coated AFM tip. X-ray Photoelectron Spectroscopy (XPS) was performed to characterize the surface chemistry of the substrate. Force distance curves were measured between the PEG-NH2, sbnd OH and sbnd OCH3 functionalized atomic force microscope (AFM) tip and the non-polar single crystalline Al2O3(11-20) surface. The experimental results exhibit non-equilibrium desorption events which hint at acid-base interactions of the electron donating hydroxyl and amino groups with Al-ions in the surface of the oxide. The observed desorption forces for the sbnd NH2, sbnd OH/Al2O3(11-20) were in the range of 100-200 pN.

Yeast cytochrome c integrated with electronic elements: a nanoscopic and spectroscopic study down to single-molecule level

NASA Astrophysics Data System (ADS)

Delfino, I.; Bonanni, B.; Andolfi, L.; Baldacchini, C.; Bizzarri, A. R.; Cannistraro, S.

2007-06-01

Various aspects of redox protein integration with nano-electronic elements are addressed by a multi-technique investigation of different yeast cytochrome c (YCC)-based hybrid systems. Three different immobilization strategies on gold via organic linkers are explored, involving either covalent bonding or electrostatic interaction. Specifically, Au surfaces are chemically modified by self-assembled monolayers (SAMs) exposing thiol-reactive groups, or by acid-oxidized single-wall carbon nanotubes (SWNTs). Atomic force microscopy and scanning tunnelling microscopy are employed to characterize the morphology and the electronic properties of single YCC molecules adsorbed on the modified gold surfaces. In each hybrid system, the protein molecules are stably assembled, in a native configuration. A standing-up arrangement of YCC on SAMs is suggested, together with an enhancement of the molecular conduction, as compared to YCC directly assembled on gold. The electrostatic interaction with functionalized SWNTs allows several YCC adsorption geometries, with a preferential high-spin haem configuration, as outlined by Raman spectroscopy. Moreover, the conduction properties of YCC, explored in different YCC nanojunctions by conductive atomic force microscopy, indicate the effectiveness of electrical conduction through the molecule and its dependence on the electrode material. The joint employment of several techniques confirms the key role of a well-designed immobilization strategy, for optimizing biorecognition capabilities and electrical coupling with conductive substrates at the single-molecule level, as a starting point for advanced applications in nano-biotechnology.

Mapping mechanical force propagation through biomolecular complexes

DOE PAGES

Schoeler, Constantin; Bernardi, Rafael C.; Malinowska, Klara H.; ...

2015-08-11

In this paper, we employ single-molecule force spectroscopy with an atomic force microscope (AFM) and steered molecular dynamics (SMD) simulations to reveal force propagation pathways through a mechanically ultrastable multidomain cellulosome protein complex. We demonstrate a new combination of network-based correlation analysis supported by AFM directional pulling experiments, which allowed us to visualize stiff paths through the protein complex along which force is transmitted. Finally, the results implicate specific force-propagation routes nonparallel to the pulling axis that are advantageous for achieving high dissociation forces.

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

PubMed Central

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

2015-01-01

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 predicteddual binding modes across multiple bacterial species, our approach opens up newpossibilities for understanding assembly and catalytic properties of a broadrange of multi-enzyme complexes. DOI: http://dx.doi.org/10.7554/eLife.10319.001 PMID:26519733

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

PubMed

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.

Single-molecule height measurements on microsomal cytochrome P450 in nanometer-scale phospholipid bilayer disks

NASA Astrophysics Data System (ADS)

Bayburt, Timothy H.; Sligar, Stephen G.

2002-05-01

The architecture of membrane proteins in their native environment of the phospholipid bilayer is critical for understanding physiological function, but has been difficult to realize experimentally. In this communication we describe the incorporation of a membrane-anchored protein into a supported phospholipid bilayer. Cytochrome P450 2B4 solubilized and purified from the hepatic endoplasmic reticulum was incorporated into phospholipid bilayer nanostructures and oriented on a surface for visualization by atomic force microscopy. Individual P450 molecules were observed protruding from the bilayer surface. Problems associated with deformation of the protein by the atomic force microscopy probe were avoided by analyzing force-dependent height measurements to quantitate the height of the protein above the bilayer surface. Measurements of the atomic force microscopy cantilever deflection as a function of probe-sample separation reveal that the top of the P450 opposite the N-terminal membrane anchor region sits 3.5 nanometers above the phospholipid-water boundary. Models of the orientation of the enzyme are presented and discussed in relation to membrane interactions and interaction with cytochrome P450 reductase.

Set-up of a high-resolution 300 mK atomic force microscope in an ultra-high vacuum compatible {sup 3}He/10 T cryostat

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

Allwörden, H. von; Ruschmeier, K.; Köhler, A.

The design of an atomic force microscope with an all-fiber interferometric detection scheme capable of atomic resolution at about 500 mK is presented. The microscope body is connected to a small pumped {sup 3}He reservoir with a base temperature of about 300 mK. The bakeable insert with the cooling stage can be moved from its measurement position inside the bore of a superconducting 10 T magnet into an ultra-high vacuum chamber, where the tip and sample can be exchanged in situ. Moreover, single atoms or molecules can be evaporated onto a cold substrate located inside the microscope. Two side chambersmore » are equipped with standard surface preparation and surface analysis tools. The performance of the microscope at low temperatures is demonstrated by resolving single Co atoms on Mn/W(110) and by showing atomic resolution on NaCl(001).« less

Molecular mechanism of extreme mechanostability in a pathogen adhesin.

PubMed

Milles, Lukas F; Schulten, Klaus; Gaub, Hermann E; Bernardi, Rafael C

2018-03-30

High resilience to mechanical stress is key when pathogens adhere to their target and initiate infection. Using atomic force microscopy-based single-molecule force spectroscopy, we explored the mechanical stability of the prototypical staphylococcal adhesin SdrG, which targets a short peptide from human fibrinogen β. Steered molecular dynamics simulations revealed, and single-molecule force spectroscopy experiments confirmed, the mechanism by which this complex withstands forces of over 2 nanonewtons, a regime previously associated with the strength of a covalent bond. The target peptide, confined in a screwlike manner in the binding pocket of SdrG, distributes forces mainly toward the peptide backbone through an intricate hydrogen bond network. Thus, these adhesins can attach to their target with exceptionally resilient mechanostability, virtually independent of peptide side chains. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Surface force analysis of glycine adsorption on different crystal surfaces of titanium dioxide (TiO2).

PubMed

Ganbaatar, Narangerel; Imai, Kanae; Yano, Taka-Aki; Hara, Masahiko

2017-01-01

Surface force analysis with atomic force microscope (AFM) in which a single amino acid residue was mounted on the tip apex of AFM probe was carried out for the first time at the molecular level on titanium dioxide (TiO 2 ) as a representative mineral surface for prebiotic chemical evolution reactions. The force analyses on surfaces with three different crystal orientations revealed that the TiO 2 (110) surface has unique characteristics for adsorbing glycine molecules showing different features compared to those on TiO 2 (001) and (100). To examine this difference, we investigated thermal desorption spectroscopy (TDS) and the interaction between the PEG cross-linker and the three TiO 2 surfaces. Our data suggest that the different single crystal surfaces would provide different chemical evolution field for amino acid molecules.

DNA Free Energy Landscapes and RNA Nano-Self-Assembly Using Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Frey, Eric William

There is an important conceptual lesson which has long been appreciated by those who work in biophysics and related interdisciplinary fields. While the extraordinary behavior of biological matter is governed by its detailed atomic structure and random fluctuations, and is therefore difficult to predict, it can nevertheless be understood within simplified frameworks. Such frameworks model the system as consisting of only one or a few components, and model the behavior of the system as the occupation of a single state out of a small number of states available. The emerging widespread application of nanotechnology, such as atomic force microscopy (AFM), has expanded this understanding in eye-opening new levels of detail by enabling nano-scale control, measurement, and visualization of biological molecules. This thesis describes two independent projects, both of which illuminate this understanding using AFM, but which do so from very different perspectives. The organization of this thesis is as follows. Chapter 1 begins with an experimental background and introduction to AFM, and then describes our setup in both single-molecule manipulation and imaging modes. In Chapter 2, we describe the first project, the motivation for which is to extend methods for the experimental determination of the free energy landscape of a molecule. This chapter relies on the analysis of single-molecule manipulation data. Chapter 3 describes the second project, the motivation for which is to create RNA-based nano-structures suitable for future applications in living mammalian cells. This chapter relies mainly on imaging. Chapters 2 and 3 can thus be read and understood separately.

Progress in the Correlative Atomic Force Microscopy and Optical Microscopy

PubMed Central

Zhou, Lulu; Cai, Mingjun; Tong, Ti; Wang, Hongda

2017-01-01

Atomic force microscopy (AFM) has evolved from the originally morphological imaging technique to a powerful and multifunctional technique for manipulating and detecting the interactions between molecules at nanometer resolution. However, AFM cannot provide the precise information of synchronized molecular groups and has many shortcomings in the aspects of determining the mechanism of the interactions and the elaborate structure due to the limitations of the technology, itself, such as non-specificity and low imaging speed. To overcome the technical limitations, it is necessary to combine AFM with other complementary techniques, such as fluorescence microscopy. The combination of several complementary techniques in one instrument has increasingly become a vital approach to investigate the details of the interactions among molecules and molecular dynamics. In this review, we reported the principles of AFM and optical microscopy, such as confocal microscopy and single-molecule localization microscopy, and focused on the development and use of correlative AFM and optical microscopy. PMID:28441775

Visualizing the orientational dependence of an intermolecular potential

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

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

PubMed

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.

Angle-Dependent Atomic Force Microscopy Single-Chain Pulling of Adsorbed Macromolecules from Planar Surfaces Unveils the Signature of an Adsorption-Desorption Transition.

PubMed

Grebíková, Lucie; Whittington, Stuart G; Vancso, Julius G

2018-05-23

The adsorption-desorption behavior of polymer chains is at the heart of macromolecular surface science and technology. With the current developments in atomic force microscopy (AFM), it has now become possible to address the desorption problem from the perspective of a single macromolecule. Here, we report on desorption of single polymer chains on planar surfaces by AFM-based single molecule force spectroscopy (SMFS) as a function of the pulling angle with respect to the surface-normal direction. SMFS experiments were performed in water with various substrates using different polymers covalently attached to the AFM probe tip. End-grafting at the AFM tip was achieved by surface-initiated polymerization using initiator functionalized tips. We found that the desorption force increases with a decreasing pulling angle, i.e., an enhanced adhesion of the polymer chain was observed. The magnitude of the desorption force shows a weak angular dependence at pulling angles close to the surface normal. A significant increase of the force is observed at shallower pulling from a certain pulling angle. This behavior carries the signature of an adsorption-desorption transition. The angular dependence of the normalized desorption force exhibits a universal behavior. We compared and interpreted our results using theoretical predictions for single-chain adsorption-desorption transitions.

Angle-Dependent Atomic Force Microscopy Single-Chain Pulling of Adsorbed Macromolecules from Planar Surfaces Unveils the Signature of an Adsorption–Desorption Transition

PubMed Central

2018-01-01

The adsorption–desorption behavior of polymer chains is at the heart of macromolecular surface science and technology. With the current developments in atomic force microscopy (AFM), it has now become possible to address the desorption problem from the perspective of a single macromolecule. Here, we report on desorption of single polymer chains on planar surfaces by AFM-based single molecule force spectroscopy (SMFS) as a function of the pulling angle with respect to the surface-normal direction. SMFS experiments were performed in water with various substrates using different polymers covalently attached to the AFM probe tip. End-grafting at the AFM tip was achieved by surface-initiated polymerization using initiator functionalized tips. We found that the desorption force increases with a decreasing pulling angle, i.e., an enhanced adhesion of the polymer chain was observed. The magnitude of the desorption force shows a weak angular dependence at pulling angles close to the surface normal. A significant increase of the force is observed at shallower pulling from a certain pulling angle. This behavior carries the signature of an adsorption–desorption transition. The angular dependence of the normalized desorption force exhibits a universal behavior. We compared and interpreted our results using theoretical predictions for single-chain adsorption–desorption transitions. PMID:29712430

Dynamic effects in friction and adhesion through cooperative rupture and formation of supramolecular bonds.

PubMed

Blass, Johanna; Albrecht, Marcel; Bozna, Bianca L; Wenz, Gerhard; Bennewitz, Roland

2015-05-07

We introduce a molecular toolkit for studying the dynamics in friction and adhesion from the single molecule level to effects of multivalency. As experimental model system we use supramolecular bonds established by the inclusion of ditopic adamantane connector molecules into two surface-bound cyclodextrin molecules, attached to a tip of an atomic force microscope (AFM) and to a flat silicon surface. The rupture force of a single bond does not depend on the pulling rate, indicating that the fast complexation kinetics of adamantane and cyclodextrin are probed in thermal equilibrium. In contrast, the pull-off force for a group of supramolecular bonds depends on the unloading rate revealing a non-equilibrium situation, an effect discussed as the combined action of multivalency and cantilever inertia effects. Friction forces exhibit a stick-slip characteristic which is explained by the cooperative rupture of groups of host-guest bonds and their rebinding. No dependence of friction on the sliding velocity has been observed in the accessible range of velocities due to fast rebinding and the negligible delay of cantilever response in AFM lateral force measurements.

Surface conformations of an anti-ricin aptamer and its affinity for ricin determined by atomic force microscopy and surface plasmon resonance.

PubMed

Wang, B; Lou, Z; Park, B; Kwon, Y; Zhang, H; Xu, B

2015-01-07

We used atomic force microscopy (AFM) and surface plasmon resonance (SPR) to study the surface conformations of an anti-ricin aptamer and its specific binding affinity for ricin molecules. The effect of surface modification of the Au(111) substrate on the aptamer affinity was also estimated. The AFM topography images had a resolution high enough to distinguish different aptamer conformations. The specific binding site on the aptamer molecule was clearly located by the AFM recognition images. The aptamer on a Au(111) surface modified with carboxymethylated-dextran (CD) showed both similarities to and differences from the one without CD modification. The influence of CD modification was evaluated using AFM images of various aptamer conformations on the Au(111) surface. The affinity between ricin and the anti-ricin aptamer was estimated using the off-rate values measured using AFM and SPR. The SPR measurements of the ricin sample were conducted in the range from 83.3 pM to 8.33 nM, and the limit of detection was estimated as 25 pM (1.5 ng mL(-1)). The off-rate values of the ricin-aptamer interactions were estimated using both single-molecule dynamic force spectroscopy (DFS) and SPR as (7.3 ± 0.4) × 10(-4) s(-1) and (1.82 ± 0.067) × 10(-2) s(-1), respectively. The results show that single-molecule measurements can obtain different reaction parameters from bulk solution measurements. In AFM single-molecule measurements, the various conformations of the aptamer immobilized on the gold surface determined the availability of each specific binding site to the ricin molecules. The SPR bulk solution measurements averaged the signals from specific and non-specific interactions. AFM images and DFS measurements provide more specific information on the interactions of individual aptamer and ricin molecules.

Improving single molecule force spectroscopy through automated real-time data collection and quantification of experimental conditions

PubMed Central

Scholl, Zackary N.; Marszalek, Piotr E.

2013-01-01

The benefits of single molecule force spectroscopy (SMFS) clearly outweigh the challenges which include small sample sizes, tedious data collection and introduction of human bias during the subjective data selection. These difficulties can be partially eliminated through automation of the experimental data collection process for atomic force microscopy (AFM). Automation can be accomplished using an algorithm that triages usable force-extension recordings quickly with positive and negative selection. We implemented an algorithm based on the windowed fast Fourier transform of force-extension traces that identifies peaks using force-extension regimes to correctly identify usable recordings from proteins composed of repeated domains. This algorithm excels as a real-time diagnostic because it involves <30 ms computational time, has high sensitivity and specificity, and efficiently detects weak unfolding events. We used the statistics provided by the automated procedure to clearly demonstrate the properties of molecular adhesion and how these properties change with differences in the cantilever tip and protein functional groups and protein age. PMID:24001740

Non-uniform binding of single-stranded DNA binding proteins to hybrids of single-stranded DNA and single-walled carbon nanotubes observed by atomic force microscopy in air and in liquid

NASA Astrophysics Data System (ADS)

Umemura, Kazuo; Ishizaka, Kei; Nii, Daisuke; Izumi, Katsuki

2016-12-01

Using atomic force spectroscopy (AFM), we observed hybrids of single-stranded DNA (ssDNA) and single-walled carbon nanotubes (SWNTs) with or without protein molecules in air and in an aqueous solution. This is the first report of ssDNA-SWNT hybrids with proteins in solution analyzed by AFM. In the absence of protein, the height of the ssDNA-SWNT hybrids was 1.1 ± 0.3 nm and 2.4 ± 0.6 nm in air and liquid, respectively, suggesting that the ssDNA molecules adopted a flexible structure on the SWNT surface. In the presence of single-stranded DNA binding (SSB) proteins, the heights of the hybrids in air and liquid increased to 6.4 ± 3.1 nm and 10.0 ± 4.5 nm, respectively. The AFM images clearly showed binding of the SSB proteins to the ssDNA-SWNT hybrids. The morphology of the SSB-ssDNA-SWNT hybrids was non-uniform, particularly in aqueous solution. The variance of hybrid height was quantitatively estimated by cross-section analysis along the long-axis of each hybrid. The SSB-ssDNA-SWNT hybrids showed much larger variance than the ssDNA-SWNT hybrids.

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

PubMed Central

Vanommeslaeghe, K.; MacKerell, A. D.

2012-01-01

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

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

PubMed

Vanommeslaeghe, K; MacKerell, A D

2012-12-21

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

Effects of Water on the Single-Chain Elasticity of Poly(U) RNA.

PubMed

Luo, Zhonglong; Cheng, Bo; Cui, Shuxun

2015-06-09

Water, the dominant component under the physiological condition, is a complicated solvent which greatly affects the properties of solute molecules. Here, we utilize atomic force microscope-based single-molecule force spectroscopy to study the influence of water on the single-molecule elasticity of an unstructured single-stranded RNA (poly(U)). In nonpolar solvents, RNA presents its inherent elasticity, which is consistent with the theoretical single-chain elasticity calculated by quantum mechanics calculations. In aqueous buffers, however, an additional energy of 1.88 kJ/mol·base is needed for the stretching of the ssRNA chain. This energy is consumed by the bound water rearrangement (Ew) during chain elongation. Further experimental results indicate that the Ew value is uncorrelated to the salt concentrations and stretching velocity. The results obtained in an 8 M guanidine·HCl solution provide more evidence that the bound water molecules around RNA give rise to the observed deviation between aqueous and nonaqueous environments. Compared to synthetic water-soluble polymers, the value of Ew of RNA is much lower. The weak interference of water is supposed to be the precondition for the RNA secondary structure to exist in aqueous solution.

Insight into conformational changes of a single α-helix peptide molecule through stiffness measurements

NASA Astrophysics Data System (ADS)

Kageshima, Masami; Lantz, Mark A.; Jarvis, Suzanne P.; Tokumoto, Hiroshi; Takeda, Seiji; Ptak, Arkadiusz; Nakamura, Chikashi; Miyake, Jun

2001-07-01

Stiffness variations during the conformational change of a single α-helix polylysine peptide molecule were measured in a liquid environment using atomic force microscopy (AFM) with magnetic cantilever modulation. At the initial stage of the stretching process the stiffness decreased due to the breaking of hydrogen bonds and then increased due to the stretching of the helix backbone. These changes were reversible on reversal of the stretching motion. Below p K, the stiffness did not show increase on reversal, indicating that the reforming of hydrogen bonds did not take place. Conformational changes in the molecule were examined via these changes in stiffness.

Forces and Dynamics of Glucose and Inhibitor Binding to Sodium Glucose Co-transporter SGLT1 Studied by Single Molecule Force Spectroscopy*

PubMed Central

Neundlinger, Isabel; Puntheeranurak, Theeraporn; Wildling, Linda; Rankl, Christian; Wang, Lai-Xi; Gruber, Hermann J.; Kinne, Rolf K. H.; Hinterdorfer, Peter

2014-01-01

Single molecule force spectroscopy was employed to investigate the dynamics of the sodium glucose co-transporter (SGLT1) upon substrate and inhibitor binding on the single molecule level. CHO cells stably expressing rbSGLT1 were probed by using atomic force microscopy tips carrying either thioglucose, 2′-aminoethyl β-d-glucopyranoside, or aminophlorizin. Poly(ethylene glycol) (PEG) chains of different length and varying end groups were used as tether. Experiments were performed at 10, 25 and 37 °C to address different conformational states of SGLT1. Unbinding forces between ligands and SGLT1 were recorded at different loading rates by changing the retraction velocity, yielding binding probability, width of energy barrier of the binding pocket, and the kinetic off rate constant of the binding reaction. With increasing temperature, width of energy barrier and average life time increased for the interaction of SGLT1 with thioglucose (coupled via acrylamide to a long PEG) but decreased for aminophlorizin binding. The former indicates that in the membrane-bound SGLT1 the pathway to sugar translocation involves several steps with different temperature sensitivity. The latter suggests that also the aglucon binding sites for transport inhibitors have specific, temperature-sensitive conformations. PMID:24962566

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

PubMed Central

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

2011-01-01

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

Observation of DNA Molecules Using Fluorescence Microscopy and Atomic Force Microscopy

ERIC Educational Resources Information Center

Ito, Takashi

2008-01-01

This article describes experiments for an undergraduate instrumental analysis laboratory that aim to observe individual double-stranded DNA (dsDNA) molecules using fluorescence microscopy and atomic force microscopy (AFM). dsDNA molecules are observed under several different conditions to discuss their chemical and physical properties. In…

Stability, resolution, and ultra-low wear amplitude modulation atomic force microscopy of DNA: Small amplitude small set-point imaging

NASA Astrophysics Data System (ADS)

Santos, Sergio; Barcons, Victor; Christenson, Hugo K.; Billingsley, Daniel J.; Bonass, William A.; Font, Josep; Thomson, Neil H.

2013-08-01

A way to operate fundamental mode amplitude modulation atomic force microscopy is introduced which optimizes stability and resolution for a given tip size and shows negligible tip wear over extended time periods (˜24 h). In small amplitude small set-point (SASS) imaging, the cantilever oscillates with sub-nanometer amplitudes in the proximity of the sample, without the requirement of using large drive forces, as the dynamics smoothly lead the tip to the surface through the water layer. SASS is demonstrated on single molecules of double-stranded DNA in ambient conditions where sharp silicon tips (R ˜ 2-5 nm) can resolve the right-handed double helix.

DNA and RNA sequencing by nanoscale reading through programmable electrophoresis and nanoelectrode-gated tunneling and dielectric detection

DOEpatents

Lee, James W.; Thundat, Thomas G.

2005-06-14

An apparatus and method for performing nucleic acid (DNA and/or RNA) sequencing on a single molecule. The genetic sequence information is obtained by probing through a DNA or RNA molecule base by base at nanometer scale as though looking through a strip of movie film. This DNA sequencing nanotechnology has the theoretical capability of performing DNA sequencing at a maximal rate of about 1,000,000 bases per second. This enhanced performance is made possible by a series of innovations including: novel applications of a fine-tuned nanometer gap for passage of a single DNA or RNA molecule; thin layer microfluidics for sample loading and delivery; and programmable electric fields for precise control of DNA or RNA movement. Detection methods include nanoelectrode-gated tunneling current measurements, dielectric molecular characterization, and atomic force microscopy/electrostatic force microscopy (AFM/EFM) probing for nanoscale reading of the nucleic acid sequences.

Synthetic oligorotaxanes exert high forces when folding under mechanical load

NASA Astrophysics Data System (ADS)

Sluysmans, Damien; Hubert, Sandrine; Bruns, Carson J.; Zhu, Zhixue; Stoddart, J. Fraser; Duwez, Anne-Sophie

2018-01-01

Folding is a ubiquitous process that nature uses to control the conformations of its molecular machines, allowing them to perform chemical and mechanical tasks. Over the years, chemists have synthesized foldamers that adopt well-defined and stable folded architectures, mimicking the control expressed by natural systems1,2. Mechanically interlocked molecules, such as rotaxanes and catenanes, are prototypical molecular machines that enable the controlled movement and positioning of their component parts3-5. Recently, combining the exquisite complexity of these two classes of molecules, donor-acceptor oligorotaxane foldamers have been synthesized, in which interactions between the mechanically interlocked component parts dictate the single-molecule assembly into a folded secondary structure6-8. Here we report on the mechanochemical properties of these molecules. We use atomic force microscopy-based single-molecule force spectroscopy to mechanically unfold oligorotaxanes, made of oligomeric dumbbells incorporating 1,5-dioxynaphthalene units encircled by cyclobis(paraquat-p-phenylene) rings. Real-time capture of fluctuations between unfolded and folded states reveals that the molecules exert forces of up to 50 pN against a mechanical load of up to 150 pN, and displays transition times of less than 10 μs. While the folding is at least as fast as that observed in proteins, it is remarkably more robust, thanks to the mechanically interlocked structure. Our results show that synthetic oligorotaxanes have the potential to exceed the performance of natural folding proteins.

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

NASA Astrophysics Data System (ADS)

Tamma, Venkata Ananth; Huang, Fei; Nowak, Derek; Kumar Wickramasinghe, H.

2016-06-01

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.

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

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

Tamma, Venkata Ananth; Huang, Fei; Kumar Wickramasinghe, H., E-mail: hkwick@uci.edu

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 andmore » 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.« less

Single-molecule force spectroscopy study of interactions between angiotensin II type 1 receptor and different biased ligands in living cells.

PubMed

Li, Wenhui; Xu, Jiachao; Kou, Xiaolong; Zhao, Rong; Zhou, Wei; Fang, Xiaohong

2018-05-01

Angiotensin II type 1 receptor (AT1R), a typical G protein-coupled receptor, plays a key role in regulating many cardiovascular functions. Different ligands can bind with AT1R to selectively activate either G protein (Gq) or β-arrestin (β-arr) pathway, or both pathways, but the molecular mechanism is not clear yet. In this work, we used, for the first time, atomic force microscopy-based single molecule force spectroscopy (SMFS) to study the interactions of AT1R with three types of ligands, balanced ligand, Gq-biased ligand, and β-arr-biased ligand, in living cells. The results revealed their difference in binding force and binding stability. The complex of the Gq-biased ligand-AT1R overcame two energy barriers with an intermediate state during dissociation, whereas that of β-arr-biased ligand-AT1R complex overcame one energy barrier. This indicated that AT1R had different ligand-binding conformational substates and underwent different structural changes to activate downstream signaling pathways with variable agonist efficacies. Quantitative analysis of AT1R-ligand binding in living cells at the single-molecule level offers a new tool to study the molecular mechanism of AT1R biased activation. Graphical Abstract Single-molecule force measurement on the living cell expressing AT1R-eGFP with a ligand modified AFM tip (left), the dynamic force spectra of β-arrestin biased ligands-AT1R (middle), and Gq-biased ligands-AT1R (right). The complexes of β-arr-biased ligand-AT1R overcame one energy barrier, with one linear region in the spectra, whereas the Gq-biased ligand-AT1R complexes overcame two energy barriers with two linear regions.

Understanding amyloid aggregation by statistical analysis of atomic force microscopy images

NASA Astrophysics Data System (ADS)

Adamcik, Jozef; Jung, Jin-Mi; Flakowski, Jérôme; de Los Rios, Paolo; Dietler, Giovanni; Mezzenga, Raffaele

2010-06-01

The aggregation of proteins is central to many aspects of daily life, including food processing, blood coagulation, eye cataract formation disease and prion-related neurodegenerative infections. However, the physical mechanisms responsible for amyloidosis-the irreversible fibril formation of various proteins that is linked to disorders such as Alzheimer's, Creutzfeldt-Jakob and Huntington's diseases-have not yet been fully elucidated. Here, we show that different stages of amyloid aggregation can be examined by performing a statistical polymer physics analysis of single-molecule atomic force microscopy images of heat-denatured β-lactoglobulin fibrils. The atomic force microscopy analysis, supported by theoretical arguments, reveals that the fibrils have a multistranded helical shape with twisted ribbon-like structures. Our results also indicate a possible general model for amyloid fibril assembly and illustrate the potential of this approach for investigating fibrillar systems.

Single molecule imaging of RNA polymerase II using atomic force microscopy

NASA Astrophysics Data System (ADS)

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

2003-03-01

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

Precise Orientation of a Single C60 Molecule on the Tip of a Scanning Probe Microscope

NASA Astrophysics Data System (ADS)

Chiutu, C.; Sweetman, A. M.; Lakin, A. J.; Stannard, A.; Jarvis, S.; Kantorovich, L.; Dunn, J. L.; Moriarty, P.

2012-06-01

We show that the precise orientation of a C60 molecule which terminates the tip of a scanning probe microscope can be determined with atomic precision from submolecular contrast images of the fullerene cage. A comparison of experimental scanning tunneling microscopy data with images simulated using computationally inexpensive Hückel theory provides a robust method of identifying molecular rotation and tilt at the end of the probe microscope tip. Noncontact atomic force microscopy resolves the atoms of the C60 cage closest to the surface for a range of molecular orientations at tip-sample separations where the molecule-substrate interaction potential is weakly attractive. Measurements of the C60C60 pair potential acquired using a fullerene-terminated tip are in excellent agreement with theoretical predictions based on a pairwise summation of the van der Waals interactions between C atoms in each cage, i.e., the Girifalco potential [L. Girifalco, J. Phys. Chem. 95, 5370 (1991)JPCHAX0022-365410.1021/j100167a002].

Correlating single-molecule and ensemble-average measurements of peptide adsorption onto different inorganic materials.

PubMed

Kim, Seong-Oh; Jackman, Joshua A; Mochizuki, Masahito; Yoon, Bo Kyeong; Hayashi, Tomohiro; Cho, Nam-Joon

2016-06-07

The coating of solid-binding peptides (SBPs) on inorganic material surfaces holds significant potential for improved surface functionalization at nano-bio interfaces. In most related studies, the goal has been to engineer peptides with selective and high binding affinity for a target material. The role of the material substrate itself in modulating the adsorption behavior of a peptide molecule remains less explored and there are few studies that compare the interaction of one peptide with different inorganic substrates. Herein, using a combination of two experimental techniques, we investigated the adsorption of a 16 amino acid-long random coil peptide to various inorganic substrates - gold, silicon oxide, titanium oxide and aluminum oxide. Quartz crystal microbalance-dissipation (QCM-D) experiments were performed in order to measure the peptide binding affinity for inorganic solid supports at the ensemble average level, and atomic force microscopy (AFM) experiments were conducted in order to determine the adhesion force of a single peptide molecule. A positive trend was observed between the total mass uptake of attached peptide and the single-molecule adhesion force on each substrate. Peptide affinity for gold was appreciably greater than for the oxide substrates. Collectively, the results obtained in this study offer insight into the ways in which inorganic materials can differentially influence and modulate the adhesion of SBPs.

reaxFF Reactive Force Field for Disulfide Mechanochemistry, Fitted to Multireference ab Initio Data.

PubMed

Müller, Julian; Hartke, Bernd

2016-08-09

Mechanochemistry, in particular in the form of single-molecule atomic force microscopy experiments, is difficult to model theoretically, for two reasons: Covalent bond breaking is not captured accurately by single-determinant, single-reference quantum chemistry methods, and experimental times of milliseconds or longer are hard to simulate with any approach. Reactive force fields have the potential to alleviate both problems, as demonstrated in this work: Using nondeterministic global parameter optimization by evolutionary algorithms, we have fitted a reaxFF force field to high-level multireference ab initio data for disulfides. The resulting force field can be used to reliably model large, multifunctional mechanochemistry units with disulfide bonds as designed breaking points. Explorative calculations show that a significant part of the time scale gap between AFM experiments and dynamical simulations can be bridged with this approach.

Unraveling protein-protein interactions in clathrin assemblies via atomic force spectroscopy.

PubMed

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.

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

PubMed

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.

Studying Chemical Reactions, One Bond at a Time, with Single Molecule AFM Techniques

NASA Astrophysics Data System (ADS)

Fernandez, Julio M.

2008-03-01

The mechanisms by which mechanical forces regulate the kinetics of a chemical reaction are unknown. In my lecture I will demonstrate how we use single molecule force-clamp spectroscopy and protein engineering to study the effect of force on the kinetics of thiol/disulfide exchange. Reduction of disulfide bond via the thiol/disulfide exchange chemical reaction is crucial in regulating protein function and is of common occurrence in mechanically stressed proteins. While reduction is thought to proceed through a substitution nucleophilic bimolecular (SN2) reaction, the role of a mechanical force in modulating this chemical reaction is unknown. We apply a constant stretching force to single engineered disulfide bonds and measure their rate of reduction by dithiothreitol (DTT). We find that while the reduction rate is linearly dependent on the concentration of DTT, it is exponentially dependent on the applied force, increasing 10-fold over a 300 pN range. This result predicts that the disulfide bond lengthens by 0.34 å at the transition state of the thiol/disulfide exchange reaction. In addition to DTT, we also study the reduction of the engineered disulfide bond by the E. coli enzyme thioredoxin (Trx). Thioredoxins are enzymes that catalyze disulfide bond reduction in all organisms. As before, we apply a mechanical force in the range of 25-450 pN to the engineered disulfide bond substrate and monitor the reduction of these bonds by individual enzymes. In sharp contrast with the data obtained with DTT, we now observe two alternative forms of the catalytic reaction, the first requiring a reorientation of the substrate disulfide bond, causing a shortening of the substrate polypeptide by 0.76±0.07 å, and the second elongating the substrate disulfide bond by 0.21±0.01 å. These results support the view that the Trx active site regulates the geometry of the participating sulfur atoms, with sub-ångström precision, in order to achieve efficient catalysis. Single molecule atomic force microscopy (AFM) techniques, as shown here, can probe dynamic rearrangements within an enzyme's active site which cannot be resolved with any other current structural biological technique. Furthermore, our work at the single bond level directly demonstrates that thiol/disulfide exchange in proteins is a force-dependent chemical reaction. Our findings suggest that mechanical force plays a role in disulfide reduction in vivo, a property which has never been explored by traditional biochemistry. 1.-Wiita, A.P., Ainavarapu, S.R.K., Huang, H.H. and Julio M. Fernandez (2006) Force-dependent chemical kinetics of disulfide bond reduction observed with single molecule techniques. Proc Natl Acad Sci U S A. 103(19):7222-7 2.-Wiita, A.P., Perez-Jimenez, R., Walther, K.A., Gräter, F. Berne, B.J., Holmgren, A., Sanchez-Ruiz, J.M., and Fernandez, J.M. (2007) Probing the chemistry of thioredoxin catalysis with force. Nature, 450:124-7.

Mechanically adjustable single-molecule transistors and stencil mask nanofabrication of high-resolution scanning probes

NASA Astrophysics Data System (ADS)

Champagne, Alexandre

This dissertation presents the development of two original experimental techniques to probe nanoscale objects. The first one studies electronic transport in single organic molecule transistors in which the source-drain electrode spacing is mechanically adjustable. The second involves the fabrication of high-resolution scanning probe microscopy sensors using a stencil mask lithography technique. We describe the fabrication of transistors in which a single organic molecule can be incorporated. The source and drain leads of these transistors are freely suspended above a flexible substrate, and their spacing can be adjusted by bending the substrate. We detail the technology developed to carry out measurements on these samples. We study electronic transport in single C60 molecules at low temperature. We observe Coulomb blockaded transport and can resolve the discrete energy spectrum of the molecule. We are able to mechanically tune the spacing between the electrodes (over a range of 5 A) to modulate the lead-molecule coupling, and can electrostatically tune the energy levels on the molecule by up to 160 meV using a gate electrode. Initial progress in studying different transport regimes in other molecules is also discussed. We present a lithographic process that allows the deposition of metal nanostructures with a resolution down to 10 nm directly onto atomic force microscope (AFM) tips. We show that multiple layers of lithography can be deposited and aligned. We fabricate high-resolution magnetic force microscopy (MFM) probes using this method and discuss progress to fabricate other scanning probe microscopy (SPM) sensors.

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

PubMed

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.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Detection of toxins in single molecule level using deoxyribonucleic acid aptamers

USDA-ARS?s Scientific Manuscript database

Toxins in foodstuffs are always a threat to food safety Among many toxins related to food, ricin (category B toxin) from castor beans has been mentioned in some poisoning cases happened. Atomic Force Microscopy (AFM) is a widely used nanotechnology to detect biospecies in vitro and in situ. The AFM...

Atomic force microscopy as a tool to study Xenopus laevis embryo

NASA Astrophysics Data System (ADS)

Pukhlyakova, E. A.; Efremov, Yu M.; Bagrov, D. V.; Luchinskaya, N. N.; Kiryukhin, D. O.; Belousov, L. V.; Shaitan, K. V.

2012-02-01

Atomic force microscopy (AFM) has become a powerful tool for imaging biological structures (from single molecules to living cells) and carrying out measurements of their mechanical properties. AFM provides three-dimensional high-resolution images of the studied biological objects in physiological environment. However there are only few AFM investigations of fresh tissue explants and virtually no such research on a whole organism, since most researchers work with cell cultures. In the current work AFM was used to observe the surface of living and fixed embryos and to measure mechanical properties of naive embryos and embryos with overexpression of guanine nucleotide-binding protein G-alpha-13.

DNA origami-based shape IDs for single-molecule nanomechanical genotyping

NASA Astrophysics Data System (ADS)

Zhang, Honglu; Chao, Jie; Pan, Dun; Liu, Huajie; Qiang, Yu; Liu, Ke; Cui, Chengjun; Chen, Jianhua; Huang, Qing; Hu, Jun; Wang, Lianhui; Huang, Wei; Shi, Yongyong; Fan, Chunhai

2017-04-01

Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms. Using these origami shape IDs, we directly genotype single molecules of human genomic DNA with an ultrahigh resolution of ~10 nm and the multiplexing ability. Further, we determine three types of disease-associated, long-range haplotypes in samples from the Han Chinese population. Single-molecule analysis allows robust haplotyping even for samples with low labelling efficiency. We expect this generic shape ID-based nanomechanical approach to hold great potential in genetic analysis at the single-molecule level.

DNA origami-based shape IDs for single-molecule nanomechanical genotyping

PubMed Central

Zhang, Honglu; Chao, Jie; Pan, Dun; Liu, Huajie; Qiang, Yu; Liu, Ke; Cui, Chengjun; Chen, Jianhua; Huang, Qing; Hu, Jun; Wang, Lianhui; Huang, Wei; Shi, Yongyong; Fan, Chunhai

2017-01-01

Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms. Using these origami shape IDs, we directly genotype single molecules of human genomic DNA with an ultrahigh resolution of ∼10 nm and the multiplexing ability. Further, we determine three types of disease-associated, long-range haplotypes in samples from the Han Chinese population. Single-molecule analysis allows robust haplotyping even for samples with low labelling efficiency. We expect this generic shape ID-based nanomechanical approach to hold great potential in genetic analysis at the single-molecule level. PMID:28382928

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

PubMed

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.

Plasmonic welded single walled carbon nanotubes on monolayer graphene for sensing target protein

NASA Astrophysics Data System (ADS)

Kim, Jangheon; Kim, Gi Gyu; Kim, Soohyun; Jung, Wonsuk

2016-05-01

We developed plasmonic welded single walled carbon nanotubes (SWCNTs) on monolayer graphene as a biosensor to detect target antigen molecules, fc fusion protein without any treatment to generate binder groups for linker and antibody. This plasmonic welding induces atomic networks between SWCNTs as junctions containing carboxylic groups and improves the electrical sensitivity of a SWCNTs and the graphene membrane to detect target protein. We investigated generation of the atomic networks between SWCNTs by field-emission scanning electron microscopy and atomic force microscopy after plasmonic welding process. We compared the intensity ratios of D to G peaks from the Raman spectra and electrical sheet resistance of welded SWCNTs with the results of normal SWCNTs, which decreased from 0.115 to 0.086 and from 10.5 to 4.12, respectively. Additionally, we measured the drain current via source/drain voltage after binding of the antigen to the antibody molecules. This electrical sensitivity of the welded SWCNTs was 1.55 times larger than normal SWCNTs.

Depositions of molecular nanomagnets on graphene investigated with atomic force microscopy and Raman spectroscopy

NASA Astrophysics Data System (ADS)

Walker, Sean; Vojvodin, Cameron; Li, Zhi; Willick, Kyle; Tang, Xiaowu (Shirley); Baugh, Jonathan

Molecular nanomagnets display interesting quantum phenomena, and have been proposed as potential building blocks in a variety of nanoelectronic devices with applications to both quantum memory and quantum information processing. These devices often require deposition of the molecules either sparsely (e.g. for single molecule devices) or as a thin-film. Consequently, in order for these devices to be successfully realized, the nature of the interactions between nanomagnets and the surfaces on which they may be deposited needs to be understood. We have investigated the depositions of molecular nanomagnets on graphene using atomic force microscopy and Raman spectrocopy. The nanomagnets contained a range of chemical functional groups including long alkyl chains and extended π-systems of electrons. By comparing their binding affinities we learn about the nature of the interactions between the different functional groups and the graphene.

Single Molecule Science for Personalized Nanomedicine: Atomic Force Microscopy of Biopolymer-Protein Interactions

NASA Astrophysics Data System (ADS)

Hsueh, Carlin

Nanotechnology has a unique and relatively untapped utility in the fields of medicine and dentistry at the level of single-biopolymer and -molecule diagnostics. In recent years atomic force microscopy (AFM) has garnered much interest due to its ability to obtain atomic-resolution of molecular structures and probe biophysical behaviors of biopolymers and proteins in a variety of biologically significant environments. The work presented in this thesis focuses on the nanoscale manipulation and observation of biopolymers to develop an innovative technology for personalized medicine while understanding complex biological systems. These studies described here primarily use AFM to observe biopolymer interactions with proteins and its surroundings with unprecedented resolution, providing a better understanding of these systems and interactions at the nanoscale. Transcriptional profiling, the measure of messenger RNA (mRNA) abundance in a single cell, is a powerful technique that detects "behavior" or "symptoms" at the tissue and cellular level. We have sought to develop an alternative approach, using our expertise in AFM and single molecule nanotechnology, to achieve a cost-effective high throughput method for sensitive detection and profiling of subtle changes in transcript abundance. The technique does not require amplification of the mRNA sample because the AFM provides three-dimensional views of molecules with unprecedented resolution, requires minimal sample preparation, and utilizes a simple tagging chemistry on cDNA molecules. AFM images showed collagen polymers in teeth and of Drebrin-A remodeling of filamentous actin structure and mechanics. AFM was used to image collagen on exposed dentine tubules and confirmed tubule occlusion with a desensitizing prophylaxis paste by Colgate-Palmolive. The AFM also superseded other microscopy tools in resolving F-actin helix remodeling and possible cooperative binding by a neuronal actin binding protein---Drebrin-A, an interaction that can provide scientists with a better understanding of debilitating neurological diseases, such as Alzheimer's and Down Syndrome at the molecular level. These observations provide extraordinary access to the subtle signs and behavior indicating early onset of disease in cells and tissues and to the dynamics of disease development and treatment.

Analysis of Adhesive Characteristics of Asphalt Based on Atomic Force Microscopy and Molecular Dynamics Simulation.

PubMed

Xu, Meng; Yi, Junyan; Feng, Decheng; Huang, Yudong; Wang, Dongsheng

2016-05-18

Asphalt binder is a very important building material in infrastructure construction; it is commonly mixed with mineral aggregate and used to produce asphalt concrete. Owing to the large differences in physical and chemical properties between asphalt and aggregate, adhesive bonds play an important role in determining the performance of asphalt concrete. Although many types of adhesive bonding mechanisms have been proposed to explain the interaction forces between asphalt binder and mineral aggregate, few have been confirmed and characterized. In comparison with chemical interactions, physical adsorption has been considered to play a more important role in adhesive bonding between asphalt and mineral aggregate. In this study, the silicon tip of an atomic force microscope was used to represent silicate minerals in aggregate, and a nanoscale analysis of the characteristics of adhesive bonding between asphalt binder and the silicon tip was conducted via an atomic force microscopy (AFM) test and molecular dynamics (MD) simulations. The results of the measurements and simulations could help in better understanding of the bonding and debonding procedures in asphalt-aggregate mixtures during hot mixing and under traffic loading. MD simulations on a single molecule of a component of asphalt and monocrystalline silicon demonstrate that molecules with a higher atomic density and planar structure, such as three types of asphaltene molecules, can provide greater adhesive strength. However, regarding the real components of asphalt binder, both the MD simulations and AFM test indicate that the colloidal structural behavior of asphalt also has a large influence on the adhesion behavior between asphalt and silicon. A schematic model of the interaction between asphalt and silicon is presented, which can explain the effect of aging on the adhesion behavior of asphalt.

Manipulating, Reacting, and Constructing Single Molecules with a Scanning Tunneling Microscope Tip

NASA Astrophysics Data System (ADS)

Hla, S.-W.

The fascinating advances in atom and molecule manipulation with the scanning tunneling microscope (STM) tip allow scientists to fabricate artificial atomic scale structures, to study local quantum phenomena, or to probe physical and chemical properties of single atoms and molecules on surfaces. Recent achievements in individual synthesis of single molecules with the STM tip further open up an entirely new opportunities in nanoscience and technology. The STM manipulation techniques usef ul in the molecular construction are reviewed and prospects for future opportunities of single molecule chemical engineering and their possible implications to nano-scale science and technology are discussed.

An optical conveyor for molecules.

PubMed

Weinert, Franz M; Braun, Dieter

2009-12-01

Trapping single ions under vacuum allows for precise spectroscopy in atomic physics. The confinement of biological molecules in bulk water is hindered by the lack of comparably strong forces. Molecules have been immobilized to surfaces, however often with detrimental effects on their function. Here, we optically trap molecules by creating the microscale analogue of a conveyor belt: a bidirectional flow is combined with a perpendicular thermophoretic molecule drift. Arranged in a toroidal geometry, the conveyor accumulates a hundredfold excess of 5-base DNA within seconds. The concentrations of the trapped DNA scale exponentially with length, reaching trapping potential depths of 14 kT for 50 bases. The mechanism does not require microfluidics, electrodes, or surface modifications. As a result, the trap can be dynamically relocated. The optical conveyor can be used to enhance diffusion-limited surface reactions, redirect cellular signaling, observe individual biomolecules over a prolonged time, or approach single-molecule chemistry in bulk water.

Single-Molecule Microscopy and Force Spectroscopy of Membrane Proteins

NASA Astrophysics Data System (ADS)

Engel, Andreas; Janovjak, Harald; Fotiadis, Dimtrios; Kedrov, Alexej; Cisneros, David; Müller, Daniel J.

Single-molecule atomic force microscopy (AFM) provides novel ways to characterize the structure-function relationship of native membrane proteins. High-resolution AFM topographs allow observing the structure of single proteins at sub-nanometer resolution as well as their conformational changes, oligomeric state, molecular dynamics and assembly. We will review these feasibilities illustrating examples of membrane proteins in native and reconstituted membranes. Classification of individual topographs of single proteins allows understanding the principles of motions of their extrinsic domains, to learn about their local structural flexibilities and to find the entropy minima of certain conformations. Combined with the visualization of functionally related conformational changes these insights allow understanding why certain flexibilities are required for the protein to function and how structurally flexible regions allow certain conformational changes. Complementary to AFM imaging, single-molecule force spectroscopy (SMFS) experiments detect molecular interactions established within and between membrane proteins. The sensitivity of this method makes it possible to measure interactions that stabilize secondary structures such as transmembrane α-helices, polypeptide loops and segments within. Changes in temperature or protein-protein assembly do not change the locations of stable structural segments, but influence their stability established by collective molecular interactions. Such changes alter the probability of proteins to choose a certain unfolding pathway. Recent examples have elucidated unfolding and refolding pathways of membrane proteins as well as their energy landscapes.

Ligand Binding: Molecular Mechanics Calculation of the Streptavidin-Biotin Rupture Force

NASA Astrophysics Data System (ADS)

Grubmuller, Helmut; Heymann, Berthold; Tavan, Paul

1996-02-01

The force required to rupture the streptavidin-biotin complex was calculated here by computer simulations. The computed force agrees well with that obtained by recent single molecule atomic force microscope experiments. These simulations suggest a detailed multiple-pathway rupture mechanism involving five major unbinding steps. Binding forces and specificity are attributed to a hydrogen bond network between the biotin ligand and residues within the binding pocket of streptavidin. During rupture, additional water bridges substantially enhance the stability of the complex and even dominate the binding inter-actions. In contrast, steric restraints do not appear to contribute to the binding forces, although conformational motions were observed.

Characterization of mechanical unfolding intermediates of membrane proteins by coarse grained molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Yamada, Tatsuya; Mitaku, Shigeki; Yamato, Takahisa

2018-01-01

Single-molecule force spectroscopy by atomic force microscopy allows us to get insight into the mechanical unfolding of membrane proteins, and a typical experiment exhibits characteristic patterns on the force distance curves. The origin of these patterns, however, has not been fully understood yet. We performed coarse-grained simulation of the forced unfolding of halorodopsin, reproduced the characteristic features of the experimental force distance curves. A further examination near the membrane-water interface indicated the existence of a motif for the force peak formation, i.e., the occurrence of hydrophobic residues in the upper interface region and hydrophilic residues below the lower interface region.

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

Bai, Rui; Yi, Shaoqiong; Zhang, Xuejie

Highlights: • We evaluated both single molecule binding ability and expression level of 4 ICAM-1 mutations. • AFM was used to measure single-molecule binding ability on living cells. • The SNP of ICAM-1 may induce changes in expressions rather than single-molecule binding ability. - Abstract: Atherosclerosis (As) is characterized by chronic inflammation and is a major cause of human mortality. ICAM-1-mediated adhesion of leukocytes in vessel walls plays an important role in the pathogenesis of atherosclerosis. Two single nucleotide polymorphisms (SNPs) of human intercellular adhesion molecule-1 (ICAM-1), G241R and K469E, are associated with a number of inflammatory diseases. SNP inducedmore » changes in ICAM-1 function rely not only on the expression level but also on the single-molecule binding ability which may be affected by single molecule conformation variations such as protein splicing and folding. Previous studies have shown associations between G241R/K469E polymorphisms and ICAM-1 gene expression. Nevertheless, few studies have been done that focus on the single-molecule forces of the above SNPs and their ligands. In the current study, we evaluated both single molecule binding ability and expression level of 4 ICAM-1 mutations – GK (G241/K469), GE (G241/E469), RK (R241/K469) and RE (R241/E469). No difference in adhesion ability was observed via cell adhesion assay or atomic force microscopy (AFM) measurement when comparing the GK, GE, RK, or RE genotypes of ICAM-1 to each other. On the other hand, flow cytometry suggested that there was significantly higher expression of GE genotype of ICAM-1 on transfected CHO cells. Thus, we concluded that genetic susceptibility to diseases related to ICAM-1 polymorphisms, G241R or K469E, might be due to the different expressions of ICAM-1 variants rather than to the single-molecule binding ability of ICAM-1.« less

Inelastic fingerprints of hydrogen contamination in atomic gold wire systems

NASA Astrophysics Data System (ADS)

Frederiksen, Thomas; Paulsson, Magnus; Brandbyge, Mads

2007-03-01

We present series of first-principles calculations for both pure and hydrogen contaminated gold wire systems in order to investigate how such impurities can be detected. We show how a single H atom or a single H2 molecule in an atomic gold wire will affect forces and Au-Au atom distances under elongation. We further determine the corresponding evolution of the low-bias conductance as well as the inelastic contributions from vibrations. Our results indicate that the conductance of gold wires is only slightly reduced from the conductance quantum G0 = 2e2/h by the presence of a single hydrogen impurity, hence making it difficult to use the conductance itself to distinguish between various configurations. On the other hand, our calculations of the inelastic signals predict significant differences between pure and hydrogen contaminated wires, and, importantly, between atomic and molecular forms of the impurity. A detailed characterization of gold wires with a hydrogen impurity should therefore be possible from the strain dependence of the inelastic signals in the conductance.

Carbon Nanotube Devices Engineered by Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Prisbrey, Landon

This dissertation explores the engineering of carbon nanotube electronic devices using atomic force microscopy (AFM) based techniques. A possible application for such devices is an electronic interface with individual biological molecules. This single molecule biosensing application is explored both experimentally and with computational modeling. Scanning probe microscopy techniques, such as AFM, are ideal to study nanoscale electronics. These techniques employ a probe which is raster scanned above a sample while measuring probe-surface interactions as a function of position. In addition to topographical and electrostatic/magnetic surface characterization, the probe may also be used as a tool to manipulate and engineer at the nanoscale. Nanoelectronic devices built from carbon nanotubes exhibit many exciting properties including one-dimensional electron transport. A natural consequence of onedimensional transport is that a single perturbation along the conduction channel can have extremely large effects on the device's transport characteristics. This property may be exploited to produce electronic sensors with single-molecule resolution. Here we use AFM-based engineering to fabricate atomic-sized transistors from carbon nanotube network devices. This is done through the incorporation of point defects into the carbon nanotube sidewall using voltage pulses from an AFM probe. We find that the incorporation of an oxidative defect leads to a variety of possible electrical signatures including sudden switching events, resonant scattering, and breaking of the symmetry between electron and hole transport. We discuss the relationship between these different electronic signatures and the chemical structure/charge state of the defect. Tunneling through a defect-induced Coulomb barrier is modeled with numerical Verlet integration of Schrodinger's equation and compared with experimental results. Atomic-sized transistors are ideal for single-molecule applications due to their sensitivity to electric fields with very small detection volumes. In this work we demonstrate these devices as single-molecule sensors to detect individual N-(3-Dimethylaminopropyl)- N'-ethylcarbodiimide (EDC) molecules in an aqueous environment. An exciting application of these sensors is to study individual macromolecules participating in biological reactions, or undergoing conformational change. However, it is unknown whether the associated electrostatic signals exceed detection limits. We report calculations which reveal that enzymatic processes, such as substrate binding and internal protein dynamics, are detectable at the single-molecule level using existing atomic-sized transistors. Finally, we demonstrate the use of AFM-based engineering to control the function of nanoelectronic devices without creating a point defect in the sidewall of the nanotube. With a biased AFM probe we write charge patterns on a silicon dioxide surface in close proximity to a carbon nanotube device. The written charge induces image charges in the nearby electronics, and can modulate the Fermi level in a nanotube by +/-1 eV. We use this technique to induce a spatially controlled doping charge pattern in the conduction channel, and thereby reconfigure a field-effect transistor into a pn junction. Other simple charge patterns could be used to create other devices. The doping charge persists for days and can be erased and rewritten, offering a new tool for prototyping nanodevices and optimizing electrostatic doping profiles.

Manipulating molecular quantum states with classical metal atom inputs: demonstration of a single molecule NOR logic gate.

PubMed

Soe, We-Hyo; Manzano, Carlos; Renaud, Nicolas; de Mendoza, Paula; De Sarkar, Abir; Ample, Francisco; Hliwa, Mohamed; Echavarren, Antonio M; Chandrasekhar, Natarajan; Joachim, Christian

2011-02-22

Quantum states of a trinaphthylene molecule were manipulated by putting its naphthyl branches in contact with single Au atoms. One Au atom carries 1-bit of classical information input that is converted into quantum information throughout the molecule. The Au-trinaphthylene electronic interactions give rise to measurable energy shifts of the molecular electronic states demonstrating a NOR logic gate functionality. The NOR truth table of the single molecule logic gate was characterized by means of scanning tunnelling spectroscopy.

Single-Molecule Methods for Nucleotide Excision Repair: Building a System to Watch Repair in Real Time.

PubMed

Kong, Muwen; Beckwitt, Emily C; Springall, Luke; Kad, Neil M; Van Houten, Bennett

2017-01-01

Single-molecule approaches to solving biophysical problems are powerful tools that allow static and dynamic real-time observations of specific molecular interactions of interest in the absence of ensemble-averaging effects. Here, we provide detailed protocols for building an experimental system that employs atomic force microscopy and a single-molecule DNA tightrope assay based on oblique angle illumination fluorescence microscopy. Together with approaches for engineering site-specific lesions into DNA substrates, these complementary biophysical techniques are well suited for investigating protein-DNA interactions that involve target-specific DNA-binding proteins, such as those engaged in a variety of DNA repair pathways. In this chapter, we demonstrate the utility of the platform by applying these techniques in the studies of proteins participating in nucleotide excision repair. © 2017 Elsevier Inc. All rights reserved.

Unimolecular Logic Gate with Classical Input by Single Gold Atoms.

PubMed

Skidin, Dmitry; Faizy, Omid; Krüger, Justus; Eisenhut, Frank; Jancarik, Andrej; Nguyen, Khanh-Hung; Cuniberti, Gianaurelio; Gourdon, Andre; Moresco, Francesca; Joachim, Christian

2018-02-27

By a combination of solution and on-surface chemistry, we synthesized an asymmetric starphene molecule with two long anthracenyl input branches and a short naphthyl output branch on the Au(111) surface. Starting from this molecule, we could demonstrate the working principle of a single molecule NAND logic gate by selectively contacting single gold atoms by atomic manipulation to the longer branches of the molecule. The logical input "1" ("0") is defined by the interaction (noninteraction) of a gold atom with one of the input branches. The output is measured by scanning tunneling spectroscopy following the shift in energy of the electronic tunneling resonances at the end of the short branch of the molecule.

Atomic Force Microscopy for Protein Detection and Their Physicoсhemical Characterization

PubMed Central

Bukharina, Natalia S.; Archakov, Alexander I.; Ivanov, Yuri D.

2018-01-01

This review is focused on the atomic force microscopy (AFM) capabilities to study the properties of protein biomolecules and to detect the proteins in solution. The possibilities of application of a wide range of measuring techniques and modes for visualization of proteins, determination of their stoichiometric characteristics and physicochemical properties, are analyzed. Particular attention is paid to the use of AFM as a molecular detector for detection of proteins in solutions at low concentrations, and also for determination of functional properties of single biomolecules, including the activity of individual molecules of enzymes. Prospects for the development of AFM in combination with other methods for studying biomacromolecules are discussed. PMID:29642632

Direct atomic force microscopy observation of DNA tile crystal growth at the single-molecule level.

PubMed

Evans, Constantine G; Hariadi, Rizal F; Winfree, Erik

2012-06-27

While the theoretical implications of models of DNA tile self-assembly have been extensively researched and such models have been used to design DNA tile systems for use in experiments, there has been little research testing the fundamental assumptions of those models. In this paper, we use direct observation of individual tile attachments and detachments of two DNA tile systems on a mica surface imaged with an atomic force microscope (AFM) to compile statistics of tile attachments and detachments. We show that these statistics fit the widely used kinetic Tile Assembly Model and demonstrate AFM movies as a viable technique for directly investigating DNA tile systems during growth rather than after assembly.

Transition model for ricin-aptamer interactions with multiple pathways and energy barriers

NASA Astrophysics Data System (ADS)

Wang, Bin; Xu, Bingqian

2014-02-01

We develop a transition model to interpret single-molecule ricin-aptamer interactions with multiple unbinding pathways and energy barriers measured by atomic force microscopy dynamic force spectroscopy. Molecular simulations establish the relationship between binding conformations and the corresponding unbinding pathways. Each unbinding pathway follows a Bell-Evans multiple-barrier model. Markov-type transition matrices are developed to analyze the redistribution of unbinding events among the pathways under different loading rates. Our study provides detailed information about complex behaviors in ricin-aptamer unbinding events.

An integrated instrumental setup for the combination of atomic force microscopy with optical spectroscopy.

PubMed

Owen, R J; Heyes, C D; Knebel, D; Röcker, C; Nienhaus, G U

2006-07-01

In recent years, the study of single biomolecules using fluorescence microscopy and atomic force microscopy (AFM) techniques has resulted in a plethora of new information regarding the physics underlying these complex biological systems. It is especially advantageous to be able to measure the optical, topographical, and mechanical properties of single molecules simultaneously. Here an AFM is used that is especially designed for integration with an inverted optical microscope and that has a near-infrared light source (850 nm) to eliminate interference between the optical experiment and the AFM operation. The Tip Assisted Optics (TAO) system consists of an additional 100 x 100-microm(2) X-Y scanner for the sample, which can be independently and simultaneously used with the AFM scanner. This allows the offset to be removed between the confocal optical image obtained with the sample scanner and the simultaneously acquired AFM topography image. The tip can be positioned exactly into the optical focus while the user can still navigate within the AFM image for imaging or manipulation of the sample. Thus the tip-enhancement effect can be maximized and it becomes possible to perform single molecule manipulation experiments within the focus of a confocal optical image. Here this is applied to simultaneous measurement of single quantum dot fluorescence and topography with high spatial resolution. (c) 2006 Wiley Periodicals, Inc.

Kinematic cooling of molecules in a magneto-optical trap

NASA Astrophysics Data System (ADS)

Takase, Ken; Chandler, David W.; Strecker, Kevin E.

2008-05-01

We will present our current progress on a new experimental technique aimed at slowing and cooling hot molecules using a single collision with magneto-optically trapped atoms. Kinematic cooling, unlike buffer gas and sympathetic cooling, relies only on a single collision between the molecule and atom to stop the molecule in the laboratory frame. This technique has recently been demonstrated in a crossed atomic and molecular beam machine to produce 35mK samples of nitric oxide via a single collision with argon [1]. In this technique we replace the atomic beam with a sample magneto-optically trapped atoms. We are currently designing and building a new apparatus to attempt these experiments. [1] Kevin E. Strecker and David W. Chandler (to be published)

The work of titin protein folding as a major driver in muscle contraction

PubMed Central

Eckels, Edward C.; Tapia-Rojo, Rafael; Rivas-Pardo, Jamie Andrés; Fernández, Julio M.

2018-01-01

Single molecule atomic force microscopy and magnetic tweezers experiments have demonstrated that titin Ig domains are capable of folding against a pulling force, generating mechanical work which exceeds that produced by a myosin motor. We hypothesize that upon muscle activation, formation of actomyosin crossbridges reduces the force on titin causing entropic recoil of the titin polymer and triggering the folding of the titin Ig domains. In the physiological force range of 4–15 pN under which titin operates in muscle, the folding contraction of a single Ig domain can generate 200% of the work of entropic recoil, and occurs at forces which exceed the maximum stalling force of single myosin motors. Thus titin operates like a mechanical battery storing elastic energy efficiently by unfolding Ig domains, and delivering the charge back by folding when the motors are activated during a contraction. We advance the hypothesis that titin folding and myosin activation act as inextricable partners during muscle contraction. PMID:29433413

A micromachined membrane-based active probe for biomolecular mechanics measurement

NASA Astrophysics Data System (ADS)

Torun, H.; Sutanto, J.; Sarangapani, K. K.; Joseph, P.; Degertekin, F. L.; Zhu, C.

2007-04-01

A novel micromachined, membrane-based probe has been developed and fabricated as assays to enable parallel measurements. Each probe in the array can be individually actuated, and the membrane displacement can be measured with high resolution using an integrated diffraction-based optical interferometer. To illustrate its application in single-molecule mechanics experiments, this membrane probe was used to measure unbinding forces between L-selectin reconstituted in a polymer-cushioned lipid bilayer on the probe membrane and an antibody adsorbed on an atomic force microscope cantilever. Piconewton range forces between single pairs of interacting molecules were measured from the cantilever bending while using the membrane probe as an actuator. The integrated diffraction-based optical interferometer of the probe was demonstrated to have <10 fm Hz-1/2 noise floor for frequencies as low as 3 Hz with a differential readout scheme. With soft probe membranes, this low noise level would be suitable for direct force measurements without the need for a cantilever. Furthermore, the probe membranes were shown to have 0.5 µm actuation range with a flat response up to 100 kHz, enabling measurements at fast speeds.

Electrochemically assisted localized etching of ZnO single crystals in water using a catalytically active Pt-coated atomic force microscopy probe

NASA Astrophysics Data System (ADS)

Shibata, Takayuki; Yamamoto, Kota; Sasano, Junji; Nagai, Moeto

2017-09-01

This paper presents a nanofabrication technique based on the electrochemically assisted chemical dissolution of zinc oxide (ZnO) single crystals in water at room temperature using a catalytically active Pt-coated atomic force microscopy (AFM) probe. Fabricated grooves featured depths and widths of several tens and several hundreds of nanometers, respectively. The material removal rate of ZnO was dramatically improved by controlling the formation of hydrogen ions (H+) on the surface of the catalytic Pt-coated probe via oxidation of H2O molecules; this reaction can be enhanced by applying a cathodic potential to an additional Pt-wire working electrode in a three-electrode configuration. Consequently, ZnO can be dissolved chemically in water as a soluble Zn2+ species via a reaction with H+ species present in high concentrations in the immediate vicinity of the AFM tip apex.

PREFACE: Nanoelectronics, sensors and single molecule biophysics Nanoelectronics, sensors and single molecule biophysics

NASA Astrophysics Data System (ADS)

Tao, Nongjian

2012-04-01

This special section of Journal of Physics: Condensed Matter (JPCM) is dedicated to Professor Stuart M Lindsay on the occasion of his 60th birthday and in recognition of his outstanding contributions to multiple research areas, including light scattering spectroscopy, scanning probe microscopy, biophysics, solid-liquid interfaces and molecular and nanoelectronics. It contains a collection of 14 papers in some of these areas, including a feature article by Lindsay. Each paper was subject to the normal rigorous review process of JPCM. In Lindsay's paper, he discusses the next generations of hybrid chemical-CMOS devices for low cost and personalized medical diagnosis. The discussion leads to several papers on nanotechnology for biomedical applications. Kawaguchi et al report on the detection of single pollen allergen particles using electrode embedded microchannels. Stern et al describe a structural study of three-dimensional DNA-nanoparticle assemblies. Hihath et al measure the conductance of methylated DNA, and discuss the possibility of electrical detection DNA methylation. Portillo et al study the electrostatic effects on the aggregation of prion proteins and peptides with atomic force microscopy. In an effort to understand the interactions between nanostructures and cells, Lamprecht et al report on the mapping of the intracellular distribution of carbon nanotubes with a confocal Raman imaging technique, and Wang et al focus on the intracellular delivery of gold nanoparticles using fluorescence microscopy. Park and Kristic provide theoretical analysis of micro- and nano-traps and their biological applications. This section also features several papers on the fundamentals of electron transport in single atomic wires and molecular junctions. The papers by Xu et al and by Wandlowksi et al describe new methods to measure conductance and forces in single molecule junctions and metallic atomic wires. Scullion et al report on the conductance of molecules with similar lengths but different energy barrier profiles in order to elucidate electron transport in the molecular junctions. Kiguchi and Murakoshi study metallic atomic wires under electrochemical potential control. Asai reports on a theoretical study of rectification in substituted atomic wires. Finally, Weiss et al report on a new method to pattern and functionalize oxide-free germanium surfaces with self-assembled organic monolayers, which provides interfaces between inorganic semiconductors and organic molecules. Nanoelectronics, sensors and single molecule biophysics contents Biochemistry and semiconductor electronics—the next big hit for silicon?Stuart Lindsay Electrical detection of single pollen allergen particles using electrode-embedded microchannelsChihiro Kawaguchi, Tetsuya Noda, Makusu Tsutsui, Masateru Taniguchi, Satoyuki Kawano and Tomoji Kawai Quasi 3D imaging of DNA-gold nanoparticle tetrahedral structuresAvigail Stern, Dvir Rotem, Inna Popov and Danny Porath Effects of cytosine methylation on DNA charge transportJoshua Hihath, Shaoyin Guo, Peiming Zhang and Nongjian Tao Effect of electrostatics on aggregation of prion protein Sup35 peptideAlexander M Portillo, Alexey V Krasnoslobodtsev and Yuri L Lyubchenko Mapping the intracellular distribution of carbon nanotubes after targeted delivery to carcinoma cells using confocal Raman imaging as a label-free techniqueC Lamprecht, N Gierlinger, E Heister, B Unterauer, B Plochberger, M Brameshuber, P Hinterdorfer, S Hild and A Ebner Caveolae-mediated endocytosis of biocompatible gold nanoparticles in living Hela cellsXian Hao, Jiazhen Wu, Yuping Shan, Mingjun Cai, Xin Shang, Junguang Jiang and Hongda Wang Stability of an aqueous quadrupole micro-trapJae Hyun Park and Predrag S Krstić Electron transport properties of single molecular junctions under mechanical modulationsJianfeng Zhou, Cunlan Guo and Bingqian Xu An approach to measure electromechanical properties of atomic and molecular junctionsIlya V Pobelov, Gábor Mészáros, Koji Yoshida, Artem Mishchenko, Murat Gulcur, Martin R Bryce and Thomas Wandlowski Single-molecule conductance determinations on HS(CH2)4O(CH2)4SH and HS(CH2)2O(CH2)2O(CH2)2SH, and comparison with alkanedithiols of the same lengthLisa E Scullion, Edmund Leary, Simon J Higgins and Richard J Nichols Metal atomic contact under electrochemical potential controlManabu Kiguchi and Kei Murakoshi Rectification in substituted atomic wires: a theoretical insightYoshihiro Asai High-fidelity chemical patterning on oxide-free germaniumJ Nathan Hohman, Moonhee Kim, Jeffrey A Lawrence, Patrick D McClanahan and Paul S Weiss

'Single molecule': theory and experiments, an introduction

PubMed Central

2013-01-01

At scales below micrometers, Brownian motion dictates most of the behaviors. The simple observation of a colloid is striking: a permanent and random motion is seen, whereas inertial forces play a negligible role. This Physics, where velocity is proportional to force, has opened new horizons in biology. The random feature is challenged in living systems where some proteins - molecular motors - have a directed motion whereas their passive behaviors of colloid should lead to a Brownian motion. Individual proteins, polymers of living matter such as DNA, RNA, actin or microtubules, molecular motors, all these objects can be viewed as chains of colloids. They are submitted to shocks from molecules of the solvent. Shapes taken by these biopolymers or dynamics imposed by motors can be measured and modeled from single molecules to their collective effects. Thanks to the development of experimental methods such as optical tweezers, Atomic Force Microscope (AFM), micropipettes, and quantitative fluorescence (such as Förster Resonance Energy Transfer, FRET), it is possible to manipulate these individual biomolecules in an unprecedented manner: experiments allow to probe the validity of models; and a new Physics has thereby emerged with original biological insights. Theories based on statistical mechanics are needed to explain behaviors of these systems. When force-extension curves of these molecules are extracted, the curves need to be fitted with models that predict the deformation of free objects or submitted to a force. When velocity of motors is altered, a quantitative analysis is required to explain the motions of individual molecules under external forces. This lecture will give some elements of introduction to the lectures of the session 'Nanophysics for Molecular Biology'. PMID:24565227

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

PubMed

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

2015-12-01

Atomic force microscopy (AFM) is a useful and powerful tool to study molecular interactions applied to nanomedicine. The aim of the present study was to implement a hands-on atomic AFM course for graduated biosciences and medical students. The course comprises two distinct practical sessions, where students get in touch with the use of an atomic force microscope by performing AFM scanning images of human blood cells and force spectroscopy measurements of the fibrinogen-platelet interaction. Since the beginning of this course, in 2008, the overall rating by the students was 4.7 (out of 5), meaning a good to excellent evaluation. Students were very enthusiastic and produced high-quality AFM images and force spectroscopy data. The implementation of the hands-on AFM course was a success, giving to the students the opportunity of contact with a technique that has a wide variety of applications on the nanomedicine field. In the near future, nanomedicine will have remarkable implications in medicine regarding the definition, diagnosis, and treatment of different diseases. AFM enables students to observe single molecule interactions, enabling the understanding of molecular mechanisms of different physiological and pathological processes at the nanoscale level. Therefore, the introduction of nanomedicine courses in bioscience and medical school curricula is essential. Copyright © 2015 The American Physiological Society.

Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy.

PubMed

Heenan, Patrick R; Yu, Hao; Siewny, Matthew G W; Perkins, Thomas T

2018-03-28

Precisely quantifying the energetics that drive the folding of membrane proteins into a lipid bilayer remains challenging. More than 15 years ago, atomic force microscopy (AFM) emerged as a powerful tool to mechanically extract individual membrane proteins from a lipid bilayer. Concurrently, fluctuation theorems, such as the Jarzynski equality, were applied to deduce equilibrium free energies (ΔG 0 ) from non-equilibrium single-molecule force spectroscopy records. The combination of these two advances in single-molecule studies deduced the free-energy of the model membrane protein bacteriorhodopsin in its native lipid bilayer. To elucidate this free-energy landscape at a higher resolution, we applied two recent developments. First, as an input to the reconstruction, we used force-extension curves acquired with a 100-fold higher time resolution and 10-fold higher force precision than traditional AFM studies of membrane proteins. Next, by using an inverse Weierstrass transform and the Jarzynski equality, we removed the free energy associated with the force probe and determined the molecular free-energy landscape of the molecule under study, bacteriorhodopsin. The resulting landscape yielded an average unfolding free energy per amino acid (aa) of 1.0 ± 0.1 kcal/mol, in agreement with past single-molecule studies. Moreover, on a smaller spatial scale, this high-resolution landscape also agreed with an equilibrium measurement of a particular three-aa transition in bacteriorhodopsin that yielded 2.7 kcal/mol/aa, an unexpectedly high value. Hence, while average unfolding ΔG 0 per aa is a useful metric, the derived high-resolution landscape details significant local variation from the mean. More generally, we demonstrated that, as anticipated, the inverse Weierstrass transform is an efficient means to reconstruct free-energy landscapes from AFM data.

Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy

NASA Astrophysics Data System (ADS)

Heenan, Patrick R.; Yu, Hao; Siewny, Matthew G. W.; Perkins, Thomas T.

2018-03-01

Precisely quantifying the energetics that drive the folding of membrane proteins into a lipid bilayer remains challenging. More than 15 years ago, atomic force microscopy (AFM) emerged as a powerful tool to mechanically extract individual membrane proteins from a lipid bilayer. Concurrently, fluctuation theorems, such as the Jarzynski equality, were applied to deduce equilibrium free energies (ΔG0) from non-equilibrium single-molecule force spectroscopy records. The combination of these two advances in single-molecule studies deduced the free-energy of the model membrane protein bacteriorhodopsin in its native lipid bilayer. To elucidate this free-energy landscape at a higher resolution, we applied two recent developments. First, as an input to the reconstruction, we used force-extension curves acquired with a 100-fold higher time resolution and 10-fold higher force precision than traditional AFM studies of membrane proteins. Next, by using an inverse Weierstrass transform and the Jarzynski equality, we removed the free energy associated with the force probe and determined the molecular free-energy landscape of the molecule under study, bacteriorhodopsin. The resulting landscape yielded an average unfolding free energy per amino acid (aa) of 1.0 ± 0.1 kcal/mol, in agreement with past single-molecule studies. Moreover, on a smaller spatial scale, this high-resolution landscape also agreed with an equilibrium measurement of a particular three-aa transition in bacteriorhodopsin that yielded 2.7 kcal/mol/aa, an unexpectedly high value. Hence, while average unfolding ΔG0 per aa is a useful metric, the derived high-resolution landscape details significant local variation from the mean. More generally, we demonstrated that, as anticipated, the inverse Weierstrass transform is an efficient means to reconstruct free-energy landscapes from AFM data.

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

PubMed

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.

Electron transport in single molecules: from benzene to graphene.

PubMed

Chen, F; Tao, N J

2009-03-17

Electron movement within and between molecules--that is, electron transfer--is important in many chemical, electrochemical, and biological processes. Recent advances, particularly in scanning electrochemical microscopy (SECM), scanning-tunneling microscopy (STM), and atomic force microscopy (AFM), permit the study of electron movement within single molecules. In this Account, we describe electron transport at the single-molecule level. We begin by examining the distinction between electron transport (from semiconductor physics) and electron transfer (a more general term referring to electron movement between donor and acceptor). The relation between these phenomena allows us to apply our understanding of single-molecule electron transport between electrodes to a broad range of other electron transfer processes. Electron transport is most efficient when the electron transmission probability via a molecule reaches 100%; the corresponding conductance is then 2e(2)/h (e is the charge of the electron and h is the Planck constant). This ideal conduction has been observed in a single metal atom and a string of metal atoms connected between two electrodes. However, the conductance of a molecule connected to two electrodes is often orders of magnitude less than the ideal and strongly depends on both the intrinsic properties of the molecule and its local environment. Molecular length, means of coupling to the electrodes, the presence of conjugated double bonds, and the inclusion of possible redox centers (for example, ferrocene) within the molecular wire have a pronounced effect on the conductance. This complex behavior is responsible for diverse chemical and biological phenomena and is potentially useful for device applications. Polycyclic aromatic hydrocarbons (PAHs) afford unique insight into electron transport in single molecules. The simplest one, benzene, has a conductance much less than 2e(2)/h due to its large LUMO-HOMO gap. At the other end of the spectrum, graphene sheets and carbon nanotubes--consisting of infinite numbers of aromatic rings--have small or even zero energy gaps between the conduction and valence bands. Between these two limits are intermediate molecules with rich properties, such as perylene derivatives made of seven aromatic rings; the properties of these types of molecules have yet to be fully explored. Studying PAHs is important not only in answering fundamental questions about electron transport but also in the ongoing quest for molecular-scale electronic devices. This line of research also helps bridge the gap between electron transfer phenomena in small redox molecules and electron transport properties in nanostructures.

Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD.

PubMed

Mikulska-Ruminska, Karolina; Kulik, Andrej J; Benadiba, Carine; Bahar, Ivet; Dietler, Giovanni; Nowak, Wieslaw

2017-08-18

Contactin-4 (CNTN4) is a complex cell adhesion molecule (CAM) localized at neuronal membranes, playing a key role in maintaining the mechanical integrity and signaling properties of the synapse. CNTN4 consists of six immunoglobulin C2 type (IgC2) domains and four fibronectin type III (FnIII) domains that are shared with many other CAMs. Mutations in CNTN4 gene have been linked to various psychiatric disorders. Toward elucidating the response of this modular protein to mechanical stress, we studied its force-induced unfolding using single molecule atomic force microscopy (smAFM) and steered molecular dynamics (SMD) simulations. Extensive smAFM and SMD data both indicate the distinctive mechanical behavior of the two types of modules distinguished by unique force-extension signatures. The data also reveal the heterogeneity of the response of the individual FNIII and IgC2 modules, which presumably plays a role in the adaptability of CNTN4 to maintaining cell-cell communication and adhesion properties under different conditions. Results show that extensive sampling of force spectra, facilitated by robot-enhanced AFM, can help reveal the existence of weak stabilizing interactions between the domains of multidomain proteins, and provide insights into the nanomechanics of such multidomain or heteromeric proteins.

Single molecule unfolding and stretching of protein domains inside a solid-state nanopore by electric field.

PubMed

Freedman, Kevin J; Haq, S Raza; Edel, Joshua B; Jemth, Per; Kim, Min Jun

2013-01-01

Single molecule methods have provided a significantly new look at the behavior of biomolecules in both equilibrium and non-equilibrium conditions. Most notable are the stretching experiments performed by atomic force microscopes and laser tweezers. Here we present an alternative single molecule method that can unfold a protein domain, observed at electric fields greater than 10(6) V/m, and is fully controllable by the application of increasing voltages across the membrane of the pore. Furthermore this unfolding mechanism is characterized by measuring both the residence time of the protein within the nanopore and the current blockade. The unfolding data supports a gradual unfolding mechanism rather than the cooperative transition observed by classical urea denaturation experiments. Lastly it is shown that the voltage-mediated unfolding is a function of the stability of the protein by comparing two mutationally destabilized variants of the protein.

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

Yang Huayan; Yu Junping; Fu Guo

The interaction between integrin macrophage differentiation antigen associated with complement three receptor function (Mac-1) and intercellular adhesion molecule-1 (ICAM-1), which is controlled tightly by the ligand-binding activity of Mac-1, is central to the regulation of neutrophil adhesion in host defense. Several 'inside-out' signals and extracellular metal ions or antibodies have been found to activate Mac-1, resulting in an increased adhesiveness of Mac-1 to its ligands. However, the molecular basis for Mac-1 activation is not well understood yet. In this work, we have carried out a single-molecule study of Mac-1/ICAM-1 interaction force in living cells by atomic force microscopy (AFM). Ourmore » results showed that the binding probability and adhesion force of Mac-1 with ICAM-1 increased upon Mac-1 activation. Moreover, by comparing the dynamic force spectra of different Mac-1 mutants, we expected that Mac-1 activation is governed by the downward movement of its {alpha}7 helix.« less

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

PubMed

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

2016-03-15

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

THE ROLE OF COMPETITION EFFECT IN THE SELF-ASSEMBLY STRUCTURE OF 3,5-DIPHENYLBENZOIC ACID AND 2,2‧:6‧,2″-TERPYRIDINE-4‧-CARBOXYLIC ACID ON Ag(110)

NASA Astrophysics Data System (ADS)

Hu, Yufen; Li, Wei; Lu, Yan; Wang, Zhongping; Leng, Xinli; Liao, Qinghua; Liu, Xiaoqing; Wang, Li

The self-assembly structures of 2,2‧:6‧,2‧‧-terpyridine-4‧-carboxylic acid (C16H11N3O2; YN) molecules and 3,5-diphenylbenzoic acid (C19H14O2; YC) molecules on Ag(110) surface have been investigated by scanning tunneling microscopy (STM) and Density Functional Theory (DFT) calculation. The YC molecules form two different well-organized structures due to the π-π stacking and dipole-dipole interactions. When three C atoms of YC molecules are replaced by three N atoms to form YN molecules, the main driving force to form ordered assembly structures of YN molecule is changed to metal-organic coordination bond and hydrogen bond. The dramatic changes of main driving force between YC/Ag(110) and YN/Ag(110) system demonstrate that the N atoms are apt to form metal-organic coordination bond and hydrogen bond but dipole-dipole interactions and π-π stacking are relative to C atoms. These findings further reveal that the optimization design of organic molecules could vary the main driving force and then lead to the change of the molecular self-assembly structures.

Atomic-Resolution Transmission Electron Microscopic Movies for Study of Organic Molecules, Assemblies, and Reactions: The First 10 Years of Development.

PubMed

Nakamura, Eiichi

2017-06-20

A molecule is a quantum mechanical entity. "Watching motions and reactions of a molecule with our eyes" has therefore been a dream of chemists for a century. This dream has come true with the aid of the movies of atomic-resolution transmission electron microscopic (AR-TEM) molecular images through real-time observation of dynamic motions of single organic molecules (denoted hereafter as single-molecule atomic-resolution real-time (SMART) TEM imaging). Since 2007, we have reported movies of a variety of single organic molecules, organometallic molecules, and their assemblies, which are rotating, stretching, and reacting. Like movies in the theater, the atomic-resolution molecular movies provide us information on the 3-D structures of the molecules and also their time evolution. The success of the SMART-TEM imaging crucially depends on the development of "chemical fishhooks" with which fish (organic molecules) in solution can be captured on a single-walled carbon nanotube (CNT, serving as a "fishing rod"). The captured molecules are connected to a slowly vibrating CNT, and their motions are displayed on a monitor in real time. A "fishing line" connecting the fish and the rod may be a σ-bond, a van der Waals force, or other weak connections. Here, the molecule/CNT system behaves as a coupled oscillator, where the low-frequency anisotropic vibration of the CNT is transmitted to the molecules via the weak chemical connections that act as an energy filter. Interpretation of the observed motions of the molecules at atomic resolution needs us to consider the quantum mechanical nature of electrons as well as bond rotation, letting us deviate from the conventional statistical world of chemistry. What new horizons can we explore? We have so far carried out conformational studies of individual molecules, assigning anti or gauche conformations to each C-C bond in conformers that we saw. We can also determine the structures of van der Waals assemblies of organic molecules, thereby providing mechanistic insights into crystal formation-phenomena of general significance in science, engineering, and our daily life. Whereas many of the single organic molecules in a vacuum seen by SMART-TEM are sufficiently long-lived for detailed studies, molecules with low ionization potentials (<6 eV) were found to undergo chemical reactions, for example, [60]fullerene and organometallic compounds possibly via a hole catalysis mechanism, where a radical cation of CNT generated under electron irradiation catalyzes the transformation via an electron transfer mechanism. Common organic molecules whose ionization potentials are much higher (>8 eV) than that of CNT (5 eV) remain stable for a time long enough for observation at 60-120 kV acceleration voltage, as they are not oxidized by the CNT radical cation. Alternatively, the reaction may have taken place via an excited state of a molecule produced by energy transfer from CNT possessing excess energy provided by the electron beam. SMART-TEM imaging is a simple approach to the study of the structures and reactions of molecules and their assemblies and will serve as a gateway to the research and education of the science connecting the quantum mechanical world and the real world.

Single-molecule experiments in biological physics: methods and applications.

PubMed

Ritort, F

2006-08-16

I review single-molecule experiments (SMEs) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SMEs it is possible to manipulate molecules one at a time and measure distributions describing molecular properties, characterize the kinetics of biomolecular reactions and detect molecular intermediates. SMEs provide additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SMEs it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level, emphasizing the importance of SMEs to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SMEs from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOTs), magnetic tweezers (MTs), biomembrane force probes (BFPs) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation) and proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SMEs to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.

TOPICAL REVIEW: Single-molecule experiments in biological physics: methods and applications

NASA Astrophysics Data System (ADS)

Ritort, F.

2006-08-01

I review single-molecule experiments (SMEs) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SMEs it is possible to manipulate molecules one at a time and measure distributions describing molecular properties, characterize the kinetics of biomolecular reactions and detect molecular intermediates. SMEs provide additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SMEs it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level, emphasizing the importance of SMEs to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SMEs from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOTs), magnetic tweezers (MTs), biomembrane force probes (BFPs) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation) and proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SMEs to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.

High-throughput single-molecule force spectroscopy for membrane proteins

NASA Astrophysics Data System (ADS)

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.

A novel single-stranded DNA detection method based on organic semiconductor heterojunction

NASA Astrophysics Data System (ADS)

Gu, Wen; Liu, Hongbo; Zhang, Xia; Zhang, Hao; Chen, Xiong; Wang, Jun

2016-12-01

We demonstrate a novel DNA detection method with low-cost and disposable advantages by utilizing F16CuPc/CuPc planar organic heterojunction device. Single-stranded DNA (ssDNA) molecules have been well immobilized on the surface of CuPc film observed by atomic force microscopy, producing an obvious electrical response of the device. The conductivity of the organic heterojunction film was significantly increased by ssDNA immobilization because ssDNA molecules brought additional positive charges at heterojunction interface. Furthermore, the thickness dependence of CuPc upper layer on the electrical response was studied to optimize the sensitivity. This study will be helpful for the development of organic heterojunction based biosensors.

Investigating the Mechanical Properties of Plasma von Willebrand Factor Using Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Wijeratne, Sitara; Botello, Eric; Yeh, Hui-Chun; Zhou, Zhou; Bergeron, Angela; Frey, Eric; Moake, Joel; Dong, Jing-Fei; Kiang, Ching-Hwa

2011-10-01

Single-molecule manipulation allows us to study the real-time kinetics of complex cellular processes. The mechanochemistry of different forms of von Willebrand factor (VWF) and their receptor-ligand binding kinetics can be probed by atomic force microscopy (AFM). Since plasma VWF can be activated upon shear, the structural and functional properties of VWF that are critical in mediating thrombus formation become important. Here we characterized the mechanical resistance to domain unfolding of VWF to determine its conformational states. We found the shear-induced conformational changes, hence the mechanical property, can be detected by the change in unfolding forces. The relaxation rate of such effect is much longer than expected. Our results offer an insight in establishing strategies for regulating VWF adhesion activity, increasing our understanding of surface-induced thrombosis as mediated by VWF.

Atoms and Molecules. Physical Science in Action[TM]. Schlessinger Science Library. [Videotape].

ERIC Educational Resources Information Center

2000

There are more than 20 million known substances in the universe, and they are all made of the same basic ingredients--atoms and molecules. In this fun and engaging program, kids will learn about the three main subatomic particles--protons, neutrons and electrons--as well as the forces that keep atoms and molecules together. They'll discover how…

Alkali (Li, K and Na) and alkali-earth (Be, Ca and Mg) adatoms on SiC single layer

NASA Astrophysics Data System (ADS)

Baierle, Rogério J.; Rupp, Caroline J.; Anversa, Jonas

2018-03-01

First-principles calculations within the density functional theory (DFT) have been addressed to study the energetic stability, and electronic properties of alkali and alkali-earth atoms adsorbed on a silicon carbide (SiC) single layer. We observe that all atoms are most stable (higher binding energy) on the top of a Si atom, which moves out of the plane (in the opposite direction to the adsorbed atom). Alkali atoms adsorbed give raise to two spin unpaired electronic levels inside the band gap leading the SiC single layer to exhibit n-type semiconductor properties. For alkaline atoms adsorbed there is a deep occupied spin paired electronic level inside the band gap. These finding suggest that the adsorption of alkaline and alkali-earth atoms on SiC layer is a powerful feature to functionalize two dimensional SiC structures, which can be used to produce new electronic, magnetic and optical devices as well for hydrogen and oxygen evolution reaction (HER and OER, respectively). Furthermore, we observe that the adsorption of H2 is ruled by dispersive forces (van der Waals interactions) while the O2 molecule is strongly adsorbed on the functionalized system.

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

PubMed

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.

Detection of gas molecules on single Mn adatom adsorbed graphyne: a DFT-D study

NASA Astrophysics Data System (ADS)

Lu, Zhansheng; Lv, Peng; Ma, Dongwei; Yang, Xinwei; Li, Shuo; Yang, Zongxian

2018-02-01

As one of the prominent applications in intelligent systems, gas sensing technology has attracted great interest in both industry and academia. In the current study, the pristine graphyne (GY) without and with a single Mn atom is investigated to detect the gas molecules (CO, CH4, CO2, NH3, NO and O2). The pristine GY is promising to detect O2 molecules because of its chemical adsorption on GY with large electron transfer. The great stability of the Mn/GY is found, and the Mn atom prefers to anchor at the alkyne ring as a single atom. Upon single Mn atom anchoring, the sensitivity and selectivity of GY based gas sensors is significantly improved for various molecules, except CH4. The recovery time of the Mn/GY after detecting the gas molecules may help to appraise the detection efficiency for the Mn/GY. The current study will help to understand the mechanism of detecting the gas molecules, and extend the potentially fascinating applications of GY-based materials.

Fabricating Large-Area Sheets of Single-Layer Graphene by CVD

NASA Technical Reports Server (NTRS)

Bronikowski, Michael; Manohara, Harish

2008-01-01

This innovation consists of a set of methodologies for preparing large area (greater than 1 cm(exp 2)) domains of single-atomic-layer graphite, also called graphene, in single (two-dimensional) crystal form. To fabricate a single graphene layer using chemical vapor deposition (CVD), the process begins with an atomically flat surface of an appropriate substrate and an appropriate precursor molecule containing carbon atoms attached to substituent atoms or groups. These molecules will be brought into contact with the substrate surface by being flowed over, or sprayed onto, the substrate, under CVD conditions of low pressure and elevated temperature. Upon contact with the surface, the precursor molecules will decompose. The substituent groups detach from the carbon atoms and form gas-phase species, leaving the unfunctionalized carbon atoms attached to the substrate surface. These carbon atoms will diffuse upon this surface and encounter and bond to other carbon atoms. If conditions are chosen carefully, the surface carbon atoms will arrange to form the lowest energy single-layer structure available, which is the graphene lattice that is sought. Another method for creating the graphene lattice includes metal-catalyzed CVD, in which the decomposition of the precursor molecules is initiated by the catalytic action of a catalytic metal upon the substrate surface. Another type of metal-catalyzed CVD has the entire substrate composed of catalytic metal, or other material, either as a bulk crystal or as a think layer of catalyst deposited upon another surface. In this case, the precursor molecules decompose directly upon contact with the substrate, releasing their atoms and forming the graphene sheet. Atomic layer deposition (ALD) can also be used. In this method, a substrate surface at low temperature is covered with exactly one monolayer of precursor molecules (which may be of more than one type). This is heated up so that the precursor molecules decompose and form one monolayer of the target material.

HDL particles incorporate into lipid bilayers - a combined AFM and single molecule fluorescence microscopy study.

PubMed

Plochberger, Birgit; Röhrl, Clemens; Preiner, Johannes; Rankl, Christian; Brameshuber, Mario; Madl, Josef; Bittman, Robert; Ros, Robert; Sezgin, Erdinc; Eggeling, Christian; Hinterdorfer, Peter; Stangl, Herbert; Schütz, Gerhard J

2017-11-21

The process, how lipids are removed from the circulation and transferred from high density lipoprotein (HDL) - a main carrier of cholesterol in the blood stream - to cells, is highly complex. HDL particles are captured from the blood stream by the scavenger receptor, class B, type I (SR-BI), the so-called HDL receptor. The details in subsequent lipid-transfer process, however, have not yet been completely understood. The transfer has been proposed to occur directly at the cell surface across an unstirred water layer, via a hydrophobic channel in the receptor, or after HDL endocytosis. The role of the target lipid membrane for the transfer process, however, has largely been overlooked. Here, we studied at the single molecule level how HDL particles interact with synthetic lipid membranes. Using (high-speed) atomic force microscopy and fluorescence correlation spectroscopy (FCS) we found out that, upon contact with the membrane, HDL becomes integrated into the lipid bilayer. Combined force and single molecule fluorescence microscopy allowed us to directly monitor the transfer process of fluorescently labelled amphiphilic lipid probe from HDL particles to the lipid bilayer upon contact.

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

NASA Astrophysics Data System (ADS)

Payne, Adam

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

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

NASA Astrophysics Data System (ADS)

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

2015-05-01

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

Multidomain proteins under force

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Directly measuring single-molecule heterogeneity using force spectroscopy

PubMed Central

Hinczewski, Michael; Thirumalai, D.

2016-01-01

One of the most intriguing results of single-molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active conformations. The structural differences between these conformations may be subtle, but each distinct state can be remarkably long-lived, with interconversions between states occurring only at macroscopic timescales, fractions of a second or longer. Although we now have proof of functional heterogeneity in a handful of systems—enzymes, motors, adhesion complexes—identifying and measuring it remains a formidable challenge. Here, we show that evidence of this phenomenon is more widespread than previously known, encoded in data collected from some of the most well-established single-molecule techniques: atomic force microscopy or optical tweezer pulling experiments. We present a theoretical procedure for analyzing distributions of rupture/unfolding forces recorded at different pulling speeds. This results in a single parameter, quantifying the degree of heterogeneity, and also leads to bounds on the equilibration and conformational interconversion timescales. Surveying 10 published datasets, we find heterogeneity in 5 of them, all with interconversion rates slower than 10 s−1. Moreover, we identify two systems where additional data at realizable pulling velocities is likely to find a theoretically predicted, but so far unobserved crossover regime between heterogeneous and nonheterogeneous behavior. The significance of this regime is that it will allow far more precise estimates of the slow conformational switching times, one of the least understood aspects of functional heterogeneity. PMID:27317744

The Ehrenfest force field: Topology and consequences for the definition of an atom in a molecule.

PubMed

Martín Pendás, A; Hernández-Trujillo, J

2012-10-07

The Ehrenfest force is the force acting on the electrons in a molecule due to the presence of the other electrons and the nuclei. There is an associated force field in three-dimensional space that is obtained by the integration of the corresponding Hermitian quantum force operator over the spin coordinates of all of the electrons and the space coordinates of all of the electrons but one. This paper analyzes the topology induced by this vector field and its consequences for the definition of molecular structure and of an atom in a molecule. Its phase portrait reveals: that the nuclei are attractors of the Ehrenfest force, the existence of separatrices yielding a dense partitioning of three-dimensional space into disjoint regions, and field lines connecting the attractors through these separatrices. From the numerical point of view, when the Ehrenfest force field is obtained as minus the divergence of the kinetic stress tensor, the induced topology was found to be highly sensitive to choice of gaussian basis sets at long range. Even the use of large split valence and highly uncontracted basis sets can yield spurious critical points that may alter the number of attraction basins. Nevertheless, at short distances from the nuclei, in general, the partitioning of three-dimensional space with the Ehrenfest force field coincides with that induced by the gradient field of the electron density. However, exceptions are found in molecules where the electron density yields results in conflict with chemical intuition. In these cases, the molecular graphs of the Ehrenfest force field reveal the expected atomic connectivities. This discrepancy between the definition of an atom in a molecule between the two vector fields casts some doubts on the physical meaning of the integration of Ehrenfest forces over the basins of the electron density.

Single-molecule force measurements of the polymerizing dimeric subunit of von Willebrand factor

NASA Astrophysics Data System (ADS)

Wijeratne, Sithara S.; Li, Jingqiang; Yeh, Hui-Chun; Nolasco, Leticia; Zhou, Zhou; Bergeron, Angela; Frey, Eric W.; Moake, Joel L.; Dong, Jing-fei; Kiang, Ching-Hwa

2016-01-01

Von Willebrand factor (VWF) multimers are large adhesive proteins that are essential to the initiation of hemostatic plugs at sites of vascular injury. The binding of VWF multimers to platelets, as well as VWF proteolysis, is regulated by shear stresses that alter VWF multimeric conformation. We used single molecule manipulation with atomic force microscopy (AFM) to investigate the effect of high fluid shear stress on soluble dimeric and multimeric forms of VWF. VWF dimers are the smallest unit that polymerizes to construct large VWF multimers. The resistance to mechanical unfolding with or without exposure to shear stress was used to evaluate VWF conformational forms. Our data indicate that, unlike recombinant VWF multimers (RVWF), recombinant dimeric VWF (RDVWF) unfolding force is not altered by high shear stress (100 dynes/cm2 for 3 min at 37°C ). We conclude that under the shear conditions used (100 dynes/cm2 for 3 min at 37°C ) , VWF dimers do not self-associate into a conformation analogous to that attained by sheared large VWF multimers.

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

PubMed

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.

The effect of cigarette smoke extract on thrombomodulin-thrombin binding: an atomic force microscopy study.

PubMed

Wei, Yujie; Zhang, Xuejie; Xu, Li; Yi, Shaoqiong; Li, Yi; Fang, Xiaohong; Liu, Huiliang

2012-10-01

Cigarette smoking is a well-known risk factor for cardiovascular disease. Smoking can cause vascular endothelial dysfunction and consequently trigger haemostatic activation and thrombosis. However, the mechanism of how smoking promotes thrombosis is not fully understood. Thrombosis is associated with the imbalance of the coagulant system due to endothelial dysfunction. As a vital anticoagulation cofactor, thrombomodulin (TM) located on the endothelial cell surface is able to regulate intravascular coagulation by binding to thrombin, and the binding results in thrombosis inhibition. This work focused on the effects of cigarette smoke extract (CSE) on TM-thrombin binding by atomic force microscopy (AFM) based single-molecule force spectroscopy. The results from both in vitro and live-cell experiments indicated that CSE could notably reduce the binding probability of TM and thrombin. This study provided a new approach and new evidence for studying the mechanism of thrombosis triggered by cigarette smoking.

Probing the Mechanical Properties of Plasma von Willebrand Factor Using Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Wijeratne, Sitara; Botello, Eric; Frey, Eric; Kiang, Ching-Hwa; Dong, Jing-Fei; Yeh, Hui-Chun

2010-03-01

Single-molecule manipulation allows us to study the real time kinetics of many complex cellular processes. The mechanochemistry of different forms of von Willebrand factor (VWF) and their receptor-ligand binding kinetics can be unraveled by atomic force microscopy (AFM). Since plasma VWF can be activated upon shear, the structural and functional properties of VWF are critical in mediating thrombus formation become important. Here we characterized the mechanical resistance to domain unfolding of VWF to determine the conformational states of VWF. We found the shear induced conformational, hence mechanical property changes can be detected by the change in unfolding forces. The relaxation rate of such effect is much longed than expected. This supports the model of lateral association VWF under shear stress. Our results offer an insight in establishing strategies for regulating VWF adhesion activity, increasing our understanding of surface-induced thrombosis as mediated by VWF.

Atomic-Scale Control of Electron Transport through Single Molecules

NASA Astrophysics Data System (ADS)

Wang, Y. F.; Kröger, J.; Berndt, R.; Vázquez, H.; Brandbyge, M.; Paulsson, M.

2010-04-01

Tin-phthalocyanine molecules adsorbed on Ag(111) were contacted with the tip of a cryogenic scanning tunneling microscope. Orders-of-magnitude variations of the single-molecule junction conductance were achieved by controllably dehydrogenating the molecule and by modifying the atomic structure of the surface electrode. Nonequilibrium Green’s function calculations reproduce the trend of the conductance and visualize the current flow through the junction, which is guided through molecule-electrode chemical bonds.

Non-destructive state detection for quantum logic spectroscopy of molecular ions.

PubMed

Wolf, Fabian; Wan, Yong; Heip, Jan C; Gebert, Florian; Shi, Chunyan; Schmidt, Piet O

2016-02-25

Precision laser spectroscopy of cold and trapped molecular ions is a powerful tool in fundamental physics--used, for example, in determining fundamental constants, testing for their possible variation in the laboratory, and searching for a possible electric dipole moment of the electron. However, the absence of cycling transitions in molecules poses a challenge for direct laser cooling of the ions, and for controlling and detecting their quantum states. Previously used state-detection techniques based on photodissociation or chemical reactions are destructive and therefore inefficient, restricting the achievable resolution in laser spectroscopy. Here, we experimentally demonstrate non-destructive detection of the quantum state of a single trapped molecular ion through its strong Coulomb coupling to a well controlled, co-trapped atomic ion. An algorithm based on a state-dependent optical dipole force changes the internal state of the atom according to the internal state of the molecule. We show that individual quantum states in the molecular ion can be distinguished by the strength of their coupling to the optical dipole force. We also observe quantum jumps (induced by black-body radiation) between rotational states of a single molecular ion. Using the detuning dependence of the state-detection signal, we implement a variant of quantum logic spectroscopy of a molecular resonance. Our state-detection technique is relevant to a wide range of molecular ions, and could be applied to state-controlled quantum chemistry and to spectroscopic investigations of molecules that serve as probes for interstellar clouds.

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

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

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

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

Atomic force microscopy study on crystal growth of Cu 2+-doped L-arginine phosphate monohydrate crystals

NASA Astrophysics Data System (ADS)

Geng, Y. L.; Xu, D.; Wang, Y. L.; Du, W.; Liu, H. Y.; Zhang, G. H.; Wang, X. Q.; Sun, D. L.

2005-01-01

Sub-steps and defects of the {1 0 0} planes of Cu 2+-doped L-arginine phosphate monohydrate (LAP) crystals are observed by atomic force microscopy. Formation of sub-steps is not due to the stacking faults but a result of single LAP: Cu 2+ molecule acting as growth unit. Two-dimensional (2D) nuclei with the same height as sub-steps occur on the step-edges. Impurities of Cu 2+ ions cause steps bunch and macrosteps formation. Liquid inclusions in the form of long channels form when the macrosteps lose their stability. Numerous small 3D growth hillocks are found in the channels. The extra stress induced by the 3D islands can result in dislocations and steps mismatches.

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

PubMed

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

2016-05-10

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

Nanostructure and force spectroscopy analysis of human peripheral blood CD4+ T cells using atomic force microscopy.

PubMed

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.

Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

NASA Astrophysics Data System (ADS)

Leng, Yongsheng; Krstić, Predrag S.; Wells, Jack C.; Cummings, Peter T.; Dean, David J.

2005-06-01

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as ˜100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Interaction between benzenedithiolate and gold: classical force field for chemical bonding.

PubMed

Leng, Yongsheng; Krstić, Predrag S; Wells, Jack C; Cummings, Peter T; Dean, David J

2005-06-22

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Continuous all-optical deceleration of molecular beams

NASA Astrophysics Data System (ADS)

Jayich, Andrew; Chen, Gary; Long, Xueping; Wang, Anna; Campbell, Wesley

2014-05-01

A significant impediment to generating ultracold molecules is slowing a molecular beam to velocities where the molecules can be cooled and trapped. We report on progress toward addressing this issue with a general optical deceleration technique for molecular and atomic beams. We propose addressing the molecular beam with a pump and dump pulse sequence from a mode-locked laser. The pump pulse counter-propagates with respect to the beam and drives the molecules to the excited state. The dump pulse co-propagates and stimulates emission, driving the molecules back to the ground state. This cycle transfers 2 ℏk of momentum and can generate very large optical forces, not limited by the spontaneous emission lifetime of the molecule or atom. Importantly, avoiding spontaneous emission limits the branching to dark states. This technique can later be augmented with cooling and trapping. We are working towards demonstrating this optical force by accelerating a cold atomic sample.

Force spectroscopy of quadruple H-bonded dimers by AFM: dynamic bond rupture and molecular time-temperature superposition.

PubMed

Zou, Shan; Schönherr, Holger; Vancso, G Julius

2005-08-17

We report on the application of the time-temperature superposition principle to supramolecular bond-rupture forces on the single-molecule level. The construction of force-loading rate master curves using atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) experiments carried out in situ at different temperatures allows one to extend the limited range of the experimentally accessible loading rates and hence to cross from thermodynamic nonequilibrium to quasi-equilibrium states. The approach is demonstrated for quadruple H-bonded ureido-4[1H]-pyrimidinone (UPy) moieties studied by variable-temperature SMFS in organic media. The unbinding forces of single quadruple H-bonding (UPy)2 complexes, which were identified based on a polymeric spacer strategy, were found to depend on the loading rate in the range of 5 nN/s to 500 nN/s at 301 K in hexadecane. By contrast, these rupture forces were independent of the loading rate from 5 to 200 nN/s at 330 K. These results indicate that the unbinding behavior of individual supramolecular complexes can be directly probed under both thermodynamic nonequilibrium and quasi-equilibrium conditions. On the basis of the time-temperature superposition principle, a master curve was constructed for a reference temperature of 301 K, and the crossover force (from loading-rate independent to -dependent regimes) was determined as approximately 145 pN (at a loading rate of approximately 5.6 nN/s). This approach significantly broadens the accessible loading-rate range and hence provides access to fine details of potential energy landscape of supramolecular complexes based on SMFS experiments.

Single-Molecule Interfacial Electron Transfer

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

Lu, H. Peter

This project is focused on the use of single-molecule high spatial and temporal resolved techniques to study molecular dynamics in condensed phase and at interfaces, especially, the complex reaction dynamics associated with electron and energy transfer rate processes. The complexity and inhomogeneity of the interfacial ET dynamics often present a major challenge for a molecular level comprehension of the intrinsically complex systems, which calls for both higher spatial and temporal resolutions at ultimate single-molecule and single-particle sensitivities. Combined single-molecule spectroscopy and electrochemical atomic force microscopy approaches are unique for heterogeneous and complex interfacial electron transfer systems because the static andmore » dynamic inhomogeneities can be identified and characterized by studying one molecule at a specific nanoscale surface site at a time. The goal of our project is to integrate and apply these spectroscopic imaging and topographic scanning techniques to measure the energy flow and electron flow between molecules and substrate surfaces as a function of surface site geometry and molecular structure. We have been primarily focusing on studying interfacial electron transfer under ambient condition and electrolyte solution involving both single crystal and colloidal TiO 2 and related substrates. The resulting molecular level understanding of the fundamental interfacial electron transfer processes will be important for developing efficient light harvesting systems and broadly applicable to problems in fundamental chemistry and physics. We have made significant advancement on deciphering the underlying mechanism of the complex and inhomogeneous interfacial electron transfer dynamics in dyesensitized TiO 2 nanoparticle systems that strongly involves with and regulated by molecule-surface interactions. We have studied interfacial electron transfer on TiO 2 nanoparticle surfaces by using ultrafast single-molecule spectroscopy and electrochemical AFM metal tip scanning microscopy, focusing on understanding the interfacial electron transfer dynamics at specific nanoscale electron transfer sites with high-spatially and temporally resolved topographic-and-spectroscopic characterization at individual molecule basis, characterizing single-molecule rate processes, reaction driving force, and molecule-substrate electronic coupling. One of the most significant characteristics of our new approach is that we are able to interrogate the complex interfacial electron transfer dynamics by actively pin-point energetic manipulation of the surface interaction and electronic couplings, beyond the conventional excitation and observation.« less

Analysis of STM images with pure and CO-functionalized tips: A first-principles and experimental study

NASA Astrophysics Data System (ADS)

Gustafsson, Alexander; Okabayashi, Norio; Peronio, Angelo; Giessibl, Franz J.; Paulsson, Magnus

2017-08-01

We describe a first-principles method to calculate scanning tunneling microscopy (STM) images, and compare the results to well-characterized experiments combining STM with atomic force microscopy (AFM). The theory is based on density functional theory with a localized basis set, where the wave functions in the vacuum gap are computed by propagating the localized-basis wave functions into the gap using a real-space grid. Constant-height STM images are computed using Bardeen's approximation method, including averaging over the reciprocal space. We consider copper adatoms and single CO molecules adsorbed on Cu(111), scanned with a single-atom copper tip with and without CO functionalization. The calculated images agree with state-of-the-art experiments, where the atomic structure of the tip apex is determined by AFM. The comparison further allows for detailed interpretation of the STM images.

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

PubMed

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.

Molecular determinants of cadherin ideal bond formation: Conformation-dependent unbinding on a multidimensional landscape

PubMed Central

Manibog, Kristine; Sankar, Kannan; Kim, Sun-Ae; Zhang, Yunxiang; Jernigan, Robert L.; Sivasankar, Sanjeevi

2016-01-01

Classical cadherin cell–cell adhesion proteins are essential for the formation and maintenance of tissue structures; their primary function is to physically couple neighboring cells and withstand mechanical force. Cadherins from opposing cells bind in two distinct trans conformations: strand-swap dimers and X-dimers. As cadherins convert between these conformations, they form ideal bonds (i.e., adhesive interactions that are insensitive to force). However, the biophysical mechanism for ideal bond formation is unknown. Here, we integrate single-molecule force measurements with coarse-grained and atomistic simulations to resolve the mechanistic basis for cadherin ideal bond formation. Using simulations, we predict the energy landscape for cadherin adhesion, the transition pathways for interconversion between X-dimers and strand-swap dimers, and the cadherin structures that form ideal bonds. Based on these predictions, we engineer cadherin mutants that promote or inhibit ideal bond formation and measure their force-dependent kinetics using single-molecule force-clamp measurements with an atomic force microscope. Our data establish that cadherins adopt an intermediate conformation as they shuttle between X-dimers and strand-swap dimers; pulling on this conformation induces a torsional motion perpendicular to the pulling direction that unbinds the proteins and forms force-independent ideal bonds. Torsional motion is blocked when cadherins associate laterally in a cis orientation, suggesting that ideal bonds may play a role in mechanically regulating cadherin clustering on cell surfaces. PMID:27621473

Stability investigation of a high number density Pt1/Fe2O3 single-atom catalyst under different gas environments by HAADF-STEM

NASA Astrophysics Data System (ADS)

Duan, Sibin; Wang, Rongming; Liu, Jingyue

2018-05-01

Catalysis by supported single metal atoms has demonstrated tremendous potential for practical applications due to their unique catalytic properties. Unless they are strongly anchored to the support surfaces, supported single atoms, however, are thermodynamically unstable, which poses a major obstacle for broad applications of single-atom catalysts (SACs). In order to develop strategies to improve the stability of SACs, we need to understand the intrinsic nature of the sintering processes of supported single metal atoms, especially under various gas environments that are relevant to important catalytic reactions. We report on the synthesis of high number density Pt1/Fe2O3 SACs using a facial strong adsorption method and the study of the mobility of these supported Pt single atoms at 250 °C under various gas environments that are relevant to CO oxidation, water–gas shift, and hydrogenation reactions. Under the oxidative gas environment, Fe2O3 supported Pt single atoms are stable even at high temperatures. The presence of either CO or H2 molecules in the gas environment, however, facilitates the movement of the Pt atoms. The strong interaction between CO and Pt weakens the binding between the Pt atoms and the support, facilitating the movement of the Pt single atoms. The dissociation of H2 molecules on the Pt atoms and their subsequent interaction with the oxygen species of the support surfaces dislodge the surface oxygen anchored Pt atoms, resulting in the formation of Pt clusters. The addition of H2O molecules to the CO or H2 significantly accelerates the sintering of the Fe2O3 supported Pt single atoms. An anchoring-site determined sintering mechanism is further proposed, which is related to the metal–support interaction.

Stability investigation of a high number density Pt1/Fe2O3 single-atom catalyst under different gas environments by HAADF-STEM.

PubMed

Duan, Sibin; Wang, Rongming; Liu, Jingyue

2018-05-18

Catalysis by supported single metal atoms has demonstrated tremendous potential for practical applications due to their unique catalytic properties. Unless they are strongly anchored to the support surfaces, supported single atoms, however, are thermodynamically unstable, which poses a major obstacle for broad applications of single-atom catalysts (SACs). In order to develop strategies to improve the stability of SACs, we need to understand the intrinsic nature of the sintering processes of supported single metal atoms, especially under various gas environments that are relevant to important catalytic reactions. We report on the synthesis of high number density Pt 1 /Fe 2 O 3 SACs using a facial strong adsorption method and the study of the mobility of these supported Pt single atoms at 250 °C under various gas environments that are relevant to CO oxidation, water-gas shift, and hydrogenation reactions. Under the oxidative gas environment, Fe 2 O 3 supported Pt single atoms are stable even at high temperatures. The presence of either CO or H 2 molecules in the gas environment, however, facilitates the movement of the Pt atoms. The strong interaction between CO and Pt weakens the binding between the Pt atoms and the support, facilitating the movement of the Pt single atoms. The dissociation of H 2 molecules on the Pt atoms and their subsequent interaction with the oxygen species of the support surfaces dislodge the surface oxygen anchored Pt atoms, resulting in the formation of Pt clusters. The addition of H 2 O molecules to the CO or H 2 significantly accelerates the sintering of the Fe 2 O 3 supported Pt single atoms. An anchoring-site determined sintering mechanism is further proposed, which is related to the metal-support interaction.

Direct optical mapping of transcription factor binding sites on field-stretched λ-DNA in nanofluidic devices

PubMed Central

Sriram, K. K.; Yeh, Jia-Wei; Lin, Yii-Lih; Chang, Yi-Ren; Chou, Chia-Fu

2014-01-01

Mapping transcription factor (TF) binding sites along a DNA backbone is crucial in understanding the regulatory circuits that control cellular processes. Here, we deployed a method adopting bioconjugation, nanofluidic confinement and fluorescence single molecule imaging for direct mapping of TF (RNA polymerase) binding sites on field-stretched single DNA molecules. Using this method, we have mapped out five of the TF binding sites of E. coli RNA polymerase to bacteriophage λ-DNA, where two promoter sites and three pseudo-promoter sites are identified with the corresponding binding frequency of 45% and 30%, respectively. Our method is quick, robust and capable of resolving protein-binding locations with high accuracy (∼ 300 bp), making our system a complementary platform to the methods currently practiced. It is advantageous in parallel analysis and less prone to false positive results over other single molecule mapping techniques such as optical tweezers, atomic force microscopy and molecular combing, and could potentially be extended to general mapping of protein–DNA interaction sites. PMID:24753422

Force-induced chemical reactions on the metal centre in a single metalloprotein molecule.

PubMed

Zheng, Peng; Arantes, Guilherme M; Field, Martin J; Li, Hongbin

2015-06-25

Metalloproteins play indispensable roles in biology owing to the versatile chemical reactivity of metal centres. However, studying their reactivity in many metalloproteins is challenging, as protein three-dimensional structure encloses labile metal centres, thus limiting their access to reactants and impeding direct measurements. Here we demonstrate the use of single-molecule atomic force microscopy to induce partial unfolding to expose metal centres in metalloproteins to aqueous solution, thus allowing for studying their chemical reactivity in aqueous solution for the first time. As a proof-of-principle, we demonstrate two chemical reactions for the FeS4 centre in rubredoxin: electrophilic protonation and nucleophilic ligand substitution. Our results show that protonation and ligand substitution result in mechanical destabilization of the FeS4 centre. Quantum chemical calculations corroborated experimental results and revealed detailed reaction mechanisms. We anticipate that this novel approach will provide insights into chemical reactivity of metal centres in metalloproteins under biologically more relevant conditions.

Force-induced chemical reactions on the metal centre in a single metalloprotein molecule

PubMed Central

Zheng, Peng; Arantes, Guilherme M.; Field, Martin J.; Li, Hongbin

2015-01-01

Metalloproteins play indispensable roles in biology owing to the versatile chemical reactivity of metal centres. However, studying their reactivity in many metalloproteins is challenging, as protein three-dimensional structure encloses labile metal centres, thus limiting their access to reactants and impeding direct measurements. Here we demonstrate the use of single-molecule atomic force microscopy to induce partial unfolding to expose metal centres in metalloproteins to aqueous solution, thus allowing for studying their chemical reactivity in aqueous solution for the first time. As a proof-of-principle, we demonstrate two chemical reactions for the FeS4 centre in rubredoxin: electrophilic protonation and nucleophilic ligand substitution. Our results show that protonation and ligand substitution result in mechanical destabilization of the FeS4 centre. Quantum chemical calculations corroborated experimental results and revealed detailed reaction mechanisms. We anticipate that this novel approach will provide insights into chemical reactivity of metal centres in metalloproteins under biologically more relevant conditions. PMID:26108369

Contact Forces between Single Metal Oxide Nanoparticles in Gas-Phase Applications and Processes.

PubMed

Salameh, Samir; van der Veen, Monique A; Kappl, Michael; van Ommen, J Ruud

2017-03-14

In this work we present a comprehensive experimental study to determine the contact forces between individual metal oxide nanoparticles in the gas-phase using atomic force microscopy. In addition, we determined the amount of physisorbed water for each type of particle surface. By comparing our results with mathematical models of the interaction forces, we could demonstrate that classical continuum models of van der Waals and capillary forces alone cannot sufficiently describe the experimental findings. Rather, the discrete nature of the molecules has to be considered, which leads to ordering at the interface and the occurrence of solvation forces. We demonstrate that inclusion of solvation forces in the model leads to quantitative agreement with experimental data and that tuning of the molecular order by addition of isopropanol vapor allows us to control the interaction forces between the nanoparticles.

Single-molecule techniques in biophysics: a review of the progress in methods and applications.

PubMed

Miller, Helen; Zhou, Zhaokun; Shepherd, Jack; Wollman, Adam J M; Leake, Mark C

2018-02-01

Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in 'force spectroscopy' techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.

Single-molecule techniques in biophysics: a review of the progress in methods and applications

NASA Astrophysics Data System (ADS)

Miller, Helen; Zhou, Zhaokun; Shepherd, Jack; Wollman, Adam J. M.; Leake, Mark C.

2018-02-01

Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in ‘force spectroscopy’ techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.

Isolating and moving single atoms using silicon nanocrystals

DOEpatents

Carroll, Malcolm S.

2010-09-07

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

Repurposing a Benchtop Centrifuge for High-Throughput Single-Molecule Force Spectroscopy.

PubMed

Yang, Darren; Wong, Wesley P

2018-01-01

We present high-throughput single-molecule manipulation using a benchtop centrifuge, overcoming limitations common in other single-molecule approaches such as high cost, low throughput, technical difficulty, and strict infrastructure requirements. An inexpensive and compact Centrifuge Force Microscope (CFM) adapted to a commercial centrifuge enables use by nonspecialists, and integration with DNA nanoswitches facilitates both reliable measurements and repeated molecular interrogation. Here, we provide detailed protocols for constructing the CFM, creating DNA nanoswitch samples, and carrying out single-molecule force measurements.

Cross-Sectional Imaging of Boundary Lubrication Layer Formed by Fatty Acid by Means of Frequency-Modulation Atomic Force Microscopy.

PubMed

Hirayama, Tomoko; Kawamura, Ryota; Fujino, Keita; Matsuoka, Takashi; Komiya, Hiroshi; Onishi, Hiroshi

2017-10-10

To observe in situ the adsorption of fatty acid onto metal surfaces, cross-sectional images of the adsorption layer were acquired by frequency-modulation atomic force microscopy (FM-AFM). Hexadecane and palmitic acid were used as the base oil and typical fatty acid, respectively. A Cu-coated silicon wafer was prepared as the target substrate. The solvation structure formed by hexadecane molecules at the interface between the Cu substrate and the hexadecane was observed, and the layer pitch was found to be about 0.6 nm, which corresponds to the height of hexadecane molecules. This demonstrates that hexadecane molecules physically adsorbed onto the surface due to van der Waals forces with lying orientation because hexadecane is a nonpolar hydrocarbon. When hexadecane with palmitic acid was put on the Cu substrate instead of pure hexadecane, an adsorption layer of palmitic acid was observed at the interface. The layer pitch was about 2.5-2.8 nm, which matches the chain length of palmitic acid molecules well. This indicates that the original adsorption layer was monolayer or single bilayer in the local area. In addition, a cross-sectional image captured 1 h after observation started to reveal that the adsorbed additive layer gradually grew up to be thicker than about 20 nm due to an external stimulus, such as cantilever oscillation. This is the first report of in situ observation of an adsorbed layer by FM-AFM in the tribology field and demonstrates that FM-AFM is useful for clarifying the actual boundary lubrication mechanism.

Protein mechanics: from single molecules to functional biomaterials.

PubMed

Li, Hongbin; Cao, Yi

2010-10-19

Elastomeric proteins act as the essential functional units in a wide variety of biomechanical machinery and serve as the basic building blocks for biological materials that exhibit superb mechanical properties. These proteins provide the desired elasticity, mechanical strength, resilience, and toughness within these materials. Understanding the mechanical properties of elastomeric protein-based biomaterials is a multiscale problem spanning from the atomistic/molecular level to the macroscopic level. Uncovering the design principles of individual elastomeric building blocks is critical both for the scientific understanding of multiscale mechanics of biomaterials and for the rational engineering of novel biomaterials with desirable mechanical properties. The development of single-molecule force spectroscopy techniques has provided methods for characterizing mechanical properties of elastomeric proteins one molecule at a time. Single-molecule atomic force microscopy (AFM) is uniquely suited to this purpose. Molecular dynamic simulations, protein engineering techniques, and single-molecule AFM study have collectively revealed tremendous insights into the molecular design of single elastomeric proteins, which can guide the design and engineering of elastomeric proteins with tailored mechanical properties. Researchers are focusing experimental efforts toward engineering artificial elastomeric proteins with mechanical properties that mimic or even surpass those of natural elastomeric proteins. In this Account, we summarize our recent experimental efforts to engineer novel artificial elastomeric proteins and develop general and rational methodologies to tune the nanomechanical properties of elastomeric proteins at the single-molecule level. We focus on general design principles used for enhancing the mechanical stability of proteins. These principles include the development of metal-chelation-based general methodology, strategies to control the unfolding hierarchy of multidomain elastomeric proteins, and the design of novel elastomeric proteins that exhibit stimuli-responsive mechanical properties. Moving forward, we are now exploring the use of these artificial elastomeric proteins as building blocks of protein-based biomaterials. Ultimately, we would like to rationally tailor mechanical properties of elastomeric protein-based materials by programming the molecular sequence, and thus nanomechanical properties, of elastomeric proteins at the single-molecule level. This step would help bridge the gap between single protein mechanics and material biomechanics, revealing how the mechanical properties of individual elastomeric proteins are translated into the properties of macroscopic materials.

Computational Study of Nonadiabatic Effects in Atom-Molecule Reactive Scattering.

DTIC Science & Technology

1982-11-15

a similar interpretation to those in Fig. 4-a, with the rotational effects most evident in the reactant tube (due to the mixing of the two open rotor ...AD-A125 135 COMPUTATIONAL STUDY OF NONRDIABATIC EFFECTS IN 1/2 ATOM-MOLECULE REACTIVE SCATTERING(U) CHEMICAL DYNAMICS CORP COLUMBUS OH B C GARRETT...COMPUTATIONAL STUDY OF NONADIABATIC EFFECTS [ Z IN ATOM-MOLECULE REACTIVE SCATTERING C:) TO AIR FORCE OFFICE OF SCIENTIFIC RESEARCHk CONTRACT NO. F49620-81

The scanning tunnelling microscope as an operative tool: doing physics and chemistry with single atoms and molecules.

PubMed

Rieder, Karl-Heinz; Meyer, Gerhard; Hla, Saw-Wai; Moresco, Francesca; Braun, Kai F; Morgenstern, Karina; Repp, Jascha; Foelsch, Stefan; Bartels, Ludwig

2004-06-15

The scanning tunnelling microscope, initially invented to image surfaces down to the atomic scale, has been further developed in the last few years to an operative tool, with which atoms and molecules can be manipulated at will at low substrate temperatures in different manners to create and investigate artificial structures, whose properties can be investigated employing spectroscopic dI/dV measurements. The tunnelling current can be used to selectively break chemical bonds, but also to induce chemical association. These possibilities give rise to startling new opportunities for physical and chemical experiments on the single atom and single molecule level. Here we provide a short overview on recent results obtained with these techniques.

Effect of polarization forces on carbon deposition on a non-spherical nanoparticle. Monte Carlo simulations [Effect of polarization forces on atom deposition on a non-spherical nanoparticle. Monte Carlo simulations

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

Nemchinsky, V.; Khrabry, A.

Trajectories of a polarizable species (atoms or molecules) in the vicinity of a negatively charged nanoparticle (at a floating potential) are considered. The atoms are pulled into regions of strong electric field by polarization forces. The polarization increases the deposition rate of the atoms and molecules at the nanoparticle. The effect of the non-spherical shape of the nanoparticle is investigated by the Monte Carlo method. The shape of the non-spherical nanoparticle is approximated by an ellipsoid. The total deposition rate and its flux density distribution along the nanoparticle surface are calculated. As a result, it is shown that the fluxmore » density is not uniform along the surface. It is maximal at the nanoparticle tips.« less

Effect of polarization forces on carbon deposition on a non-spherical nanoparticle. Monte Carlo simulations [Effect of polarization forces on atom deposition on a non-spherical nanoparticle. Monte Carlo simulations

DOE PAGES

Nemchinsky, V.; Khrabry, A.

2018-02-01

Trajectories of a polarizable species (atoms or molecules) in the vicinity of a negatively charged nanoparticle (at a floating potential) are considered. The atoms are pulled into regions of strong electric field by polarization forces. The polarization increases the deposition rate of the atoms and molecules at the nanoparticle. The effect of the non-spherical shape of the nanoparticle is investigated by the Monte Carlo method. The shape of the non-spherical nanoparticle is approximated by an ellipsoid. The total deposition rate and its flux density distribution along the nanoparticle surface are calculated. As a result, it is shown that the fluxmore » density is not uniform along the surface. It is maximal at the nanoparticle tips.« less

Membrane-based actuation for high-speed single molecule force spectroscopy studies using AFM.

PubMed

Sarangapani, Krishna; Torun, Hamdi; Finkler, Ofer; Zhu, Cheng; Degertekin, Levent

2010-07-01

Atomic force microscopy (AFM)-based dynamic force spectroscopy of single molecular interactions involves characterizing unbinding/unfolding force distributions over a range of pulling speeds. Owing to their size and stiffness, AFM cantilevers are adversely affected by hydrodynamic forces, especially at pulling speeds >10 microm/s, when the viscous drag becomes comparable to the unbinding/unfolding forces. To circumvent these adverse effects, we have fabricated polymer-based membranes capable of actuating commercial AFM cantilevers at speeds >or=100 microm/s with minimal viscous drag effects. We have used FLUENT, a computational fluid dynamics (CFD) software, to simulate high-speed pulling and fast actuation of AFM cantilevers and membranes in different experimental configurations. The simulation results support the experimental findings on a variety of commercial AFM cantilevers and predict significant reduction in drag forces when membrane actuators are used. Unbinding force experiments involving human antibodies using these membranes demonstrate that it is possible to achieve bond loading rates >or=10(6) pN/s, an order of magnitude greater than that reported with commercial AFM cantilevers and systems.

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

NASA Astrophysics Data System (ADS)

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 interrogate basic structure-transport relations at the single-molecule limit.

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-08-02

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

Nonlinearity, resonance, charging, and motion at the atomic scale studied with scanning tunneling microscopes

NASA Astrophysics Data System (ADS)

Tu, Xiuwen

2008-10-01

Several novel phenomena at the single-atom and single-molecule level occurring on the surfaces of single crystals were studied with home-built low temperature scanning tunneling microscopes. The results revealed intriguing properties of single atoms and single molecules, including nonlinearity, resonance, charging, and motion. First, negative differential resistance (NDR) was observed in the dI/dV spectra for single copper-phthalocyanine (CuPc) molecules adsorbed on one- and two-layer sodium bromide (NaBr), but not for single CuPc molecules adsorbed on three-layer NaBr, all grown on a NiAl(110) surface. This transition from NDR to the absence of NDR was explained as the result of competing effects in the double-barrier tunnel junction (DBTJ) and was reproduced in a calculation based on a resonant-tunneling model. Second, the nonlinearity of the STM junction due to a single manganese (Mn) atom or MnCO molecule adsorbed on a NiAl(110) surface was used to rectify microwave irradiation. The resulting rectification current was shown to be sensitive to the spin-splitting of the electronic states of the Mn atom and to the vibrations of the MnCO molecule. Next, the ordering of cesium (Cs) atoms adsorbed on a Au(111) surface and a NiAl(110) surface was imaged in real space. Because of charge transfer to the substrates, Cs adatoms were positively charged on both surfaces. Even at 12 K, Cs adatoms were able to move and adjust according to coverage. On Au(111), the Cs first layer had a quasi-hexagonal lattice and islands of the second Cs layer did not appear until the first was completed. On NiAl(110), a locally disordered Cs first layer was observed before a locally ordered layer appeared at higher coverages. The cation-pi interactions were then studied at the single molecular level. We were able to form cation-pi complexes such as Cs···DSB, Cs···DSB···Cs, Rb···DSB, and Rb···ZnEtiol controllably by manipulation with the STM tip. We could also separate these complexes controllably by voltage pulses. STM imaging and spectroscopy revealed precise information about the atomic and electronic structure of these cation-pi complexes. Finally, electron transport through single atoms and molecules in a double-barrier tunnel junction (DBTJ) was examined. Charge bistability was observed for single ZnEtioI molecules adsorbed in several different conformations on ultrathin aluminum oxide. A sudden decrease in local apparent barrier height (LABH) was observed at the onset of an adsorbate electronic orbital for single ZnEtioI molecules and Cs atoms supported by the ultrathin aluminum oxide. The resonant-tunneling model, which was proposed to explain the transition from NDR to the absence of NDR, was found useful in explaining the sudden decrease in LABH, too. NDR, bipolar tunneling, and vibronic states were also observed and discussed in the context of DBTJ.

Atomic force microscopy investigation of growth process of organic TCNQ aggregates on SiO2 and mica substrates

NASA Astrophysics Data System (ADS)

Huan, Qing; Hu, Hao; Pan, Li-Da; Xiao, Jiang; Du, Shi-Xuan; Gao, Hong-Jun

2010-08-01

Deposition patterns of tetracyanoquinodimethane (TCNQ) molecules on different surfaces are investigated by atomic force microscopy. A homemade physical vapour deposition system allows the better control of molecule deposition. Taking advantage of this system, we investigate TCNQ thin film growth on both SiO2 and mica surfaces. It is found that dense island patterns form at a high deposition rate, and a unique seahorse-like pattern forms at a low deposition rate. Growth patterns on different substrates suggest that the fractal pattern formation is dominated by molecule-molecule interaction. Finally, a phenomenal “two-branch" model is proposed to simulate the growth process of the seahorse pattern.

Water-mediated influence of a crowded environment on internal vibrations of a protein molecule.

PubMed

Kuffel, Anna; Zielkiewicz, Jan

2016-02-14

The influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described. The cross-correlation function of the collective velocities of surface atoms of two proteins was decomposed into the Fourier series. The amplitude spectrum displays a peak at low frequencies. Also, the results of principal component analysis suggest that the close presence of an additional protein molecule influences the high-amplitude, low-frequency modes in the most prominent way. This part of the spectrum covers biologically important protein motions. The neighbor-induced changes in the inner dynamics of the protein may be connected with the changes in the velocity power spectrum of interfacial water. The additional protein molecule changes the properties of solvation water and in this way it can influence the dynamics of the second protein. It is suggested that this phenomenon may be described, at first approximation, by a damped oscillator driven by an external random force. This model was successfully applied to conformationally rigid Choristoneura fumiferana antifreeze protein molecules.

Imaging modes of atomic force microscopy for application in molecular and cell biology.

PubMed

Dufrêne, Yves F; Ando, Toshio; Garcia, Ricardo; Alsteens, David; Martinez-Martin, David; Engel, Andreas; Gerber, Christoph; Müller, Daniel J

2017-04-06

Atomic force microscopy (AFM) is a powerful, multifunctional imaging platform that allows biological samples, from single molecules to living cells, to be visualized and manipulated. Soon after the instrument was invented, it was recognized that in order to maximize the opportunities of AFM imaging in biology, various technological developments would be required to address certain limitations of the method. This has led to the creation of a range of new imaging modes, which continue to push the capabilities of the technique today. Here, we review the basic principles, advantages and limitations of the most common AFM bioimaging modes, including the popular contact and dynamic modes, as well as recently developed modes such as multiparametric, molecular recognition, multifrequency and high-speed imaging. For each of these modes, we discuss recent experiments that highlight their unique capabilities.

Quantum design rules for single molecule logic gates.

PubMed

Renaud, N; Hliwa, M; Joachim, C

2011-08-28

Recent publications have demonstrated how to implement a NOR logic gate with a single molecule using its interaction with two surface atoms as logical inputs [W. Soe et al., ACS Nano, 2011, 5, 1436]. We demonstrate here how this NOR logic gate belongs to the general family of quantum logic gates where the Boolean truth table results from a full control of the quantum trajectory of the electron transfer process through the molecule by very local and classical inputs practiced on the molecule. A new molecule OR gate is proposed for the logical inputs to be also single metal atoms, one per logical input.

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

DOE PAGES

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

2017-12-21

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

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

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

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

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

Current at Metal-Organic Interfaces

NASA Astrophysics Data System (ADS)

Kern, Klaus

2012-02-01

Charge transport through atomic and molecular constrictions greatly affects the operation and performance of organic electronic devices. Much of our understanding of the charge injection and extraction processes in these systems relays on our knowledge of the electronic structure at the metal-organic interface. Despite significant experimental and theoretical advances in studying charge transport in nanoscale junctions, a microscopic understanding at the single atom/molecule level is missing. In the present talk I will present our recent results to probe directly the nanocontact between single molecules and a metal electrode using scanning probe microscopy and spectroscopy. The experiments provide unprecedented microscopic details of single molecule and atom junctions and open new avenues to study quantum critical and many body phenomena at the atomic scale. Implications for energy conversion devices and carbon based nanoelectronics will also be discussed.

Contact Forces between Single Metal Oxide Nanoparticles in Gas-Phase Applications and Processes

PubMed Central

2017-01-01

In this work we present a comprehensive experimental study to determine the contact forces between individual metal oxide nanoparticles in the gas-phase using atomic force microscopy. In addition, we determined the amount of physisorbed water for each type of particle surface. By comparing our results with mathematical models of the interaction forces, we could demonstrate that classical continuum models of van der Waals and capillary forces alone cannot sufficiently describe the experimental findings. Rather, the discrete nature of the molecules has to be considered, which leads to ordering at the interface and the occurrence of solvation forces. We demonstrate that inclusion of solvation forces in the model leads to quantitative agreement with experimental data and that tuning of the molecular order by addition of isopropanol vapor allows us to control the interaction forces between the nanoparticles. PMID:28186771

Molecule-specific determination of atomic polarizabilities with the polarizable atomic multipole model.

PubMed

Woo Kim, Hyun; Rhee, Young Min

2012-07-30

Recently, many polarizable force fields have been devised to describe induction effects between molecules. In popular polarizable models based on induced dipole moments, atomic polarizabilities are the essential parameters and should be derived carefully. Here, we present a parameterization scheme for atomic polarizabilities using a minimization target function containing both molecular and atomic information. The main idea is to adopt reference data only from quantum chemical calculations, to perform atomic polarizability parameterizations even when relevant experimental data are scarce as in the case of electronically excited molecules. Specifically, our scheme assigns the atomic polarizabilities of any given molecule in such a way that its molecular polarizability tensor is well reproduced. We show that our scheme successfully works for various molecules in mimicking dipole responses not only in ground states but also in valence excited states. The electrostatic potential around a molecule with an externally perturbing nearby charge also exhibits a near-quantitative agreement with the reference data from quantum chemical calculations. The limitation of the model with isotropic atoms is also discussed to examine the scope of its applicability. Copyright © 2012 Wiley Periodicals, Inc.

Real-time single-molecule imaging of quantum interference.

PubMed

Juffmann, Thomas; Milic, Adriana; Müllneritsch, Michael; Asenbaum, Peter; Tsukernik, Alexander; Tüxen, Jens; Mayor, Marcel; Cheshnovsky, Ori; Arndt, Markus

2012-03-25

The observation of interference patterns in double-slit experiments with massive particles is generally regarded as the ultimate demonstration of the quantum nature of these objects. Such matter-wave interference has been observed for electrons, neutrons, atoms and molecules and, in contrast to classical physics, quantum interference can be observed when single particles arrive at the detector one by one. The build-up of such patterns in experiments with electrons has been described as the "most beautiful experiment in physics". Here, we show how a combination of nanofabrication and nano-imaging allows us to record the full two-dimensional build-up of quantum interference patterns in real time for phthalocyanine molecules and for derivatives of phthalocyanine molecules, which have masses of 514 AMU and 1,298 AMU respectively. A laser-controlled micro-evaporation source was used to produce a beam of molecules with the required intensity and coherence, and the gratings were machined in 10-nm-thick silicon nitride membranes to reduce the effect of van der Waals forces. Wide-field fluorescence microscopy detected the position of each molecule with an accuracy of 10 nm and revealed the build-up of a deterministic ensemble interference pattern from single molecules that arrived stochastically at the detector. In addition to providing this particularly clear demonstration of wave-particle duality, our approach could also be used to study larger molecules and explore the boundary between quantum and classical physics.

Real-time single-molecule imaging of quantum interference

NASA Astrophysics Data System (ADS)

Juffmann, Thomas; Milic, Adriana; Müllneritsch, Michael; Asenbaum, Peter; Tsukernik, Alexander; Tüxen, Jens; Mayor, Marcel; Cheshnovsky, Ori; Arndt, Markus

2012-05-01

The observation of interference patterns in double-slit experiments with massive particles is generally regarded as the ultimate demonstration of the quantum nature of these objects. Such matter-wave interference has been observed for electrons, neutrons, atoms and molecules and, in contrast to classical physics, quantum interference can be observed when single particles arrive at the detector one by one. The build-up of such patterns in experiments with electrons has been described as the ``most beautiful experiment in physics''. Here, we show how a combination of nanofabrication and nano-imaging allows us to record the full two-dimensional build-up of quantum interference patterns in real time for phthalocyanine molecules and for derivatives of phthalocyanine molecules, which have masses of 514 AMU and 1,298 AMU respectively. A laser-controlled micro-evaporation source was used to produce a beam of molecules with the required intensity and coherence, and the gratings were machined in 10-nm-thick silicon nitride membranes to reduce the effect of van der Waals forces. Wide-field fluorescence microscopy detected the position of each molecule with an accuracy of 10 nm and revealed the build-up of a deterministic ensemble interference pattern from single molecules that arrived stochastically at the detector. In addition to providing this particularly clear demonstration of wave-particle duality, our approach could also be used to study larger molecules and explore the boundary between quantum and classical physics.

Nanostructure and force spectroscopy analysis of human peripheral blood CD4{sup +} T cells using atomic force microscopy

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

Hu Mingqian; Wang Jiongkun; Cai Jiye

2008-09-12

To date, nanoscale imaging of the morphological changes and adhesion force of CD4{sup +} 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{sup +} T cells. The AFM images revealed that the volume of activated CD4{sup +} 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 thatmore » of the unspecific force. The adhesion forces were not randomly distributed over the surface of a single activated CD4{sup +} 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.« less

Atomic force microscope characterization of self-assembly behaviors of cyclo[8] pyrrole on solid substrates

NASA Astrophysics Data System (ADS)

Xu, Hai; Zhao, Siqi; Xiong, Xiang; Jiang, Jinzhi; Xu, Wei; Zhu, Daoben; Zhang, Yi; Liang, Wenjie; Cai, Jianfeng

2017-04-01

Cyclo [8] pyrrole (CP) is a porphyrin analogue containing eight α-conjugated pyrrole units which are arranged in a nearly coplanar conformation. The π-π interactions between CP molecules lead to regular aggregations through a solution casting process. Using tapping mode atomic force microscope (AFM), we investigated the morphology of self-assembled aggregates formed by deposition of different CP solutions on different substrates. We found that in the n-butanol solution, nanofibrous structures could be formed on the silicon or mica surface. Interestingly, on the highly oriented pyrolytic graphite (HOPG) surface, or silicon and mica surface with a toluene solution, only irregular spherical structures were identified. The difference in the nanomorphology may be attributed to distinct interactions between molecule-molecule, molecule-solvent and molecule-substrate.

Interaction of an anticancer peptide fragment of azurin with p53 and its isolated domains studied by atomic force spectroscopy.

PubMed

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.

Interaction of an anticancer peptide fragment of azurin with p53 and its isolated domains studied by atomic force spectroscopy

PubMed Central

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. PMID:22162658

CO tip functionalization in subatomic resolution atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Minjung; Chelikowsky, James R.

2015-10-01

Noncontact atomic force microscopy (nc-AFM) employing a CO-functionalized tip displays dramatically enhanced resolution wherein covalent bonds of polycyclic aromatic hydrocarbon can be imaged. Employing real-space pseudopotential first-principles calculations, we examine the role of CO in functionalizing the nc-AFM tip. Our calculations allow us to simulate full AFM images and ascertain the enhancement mechanism of the CO molecule. We consider two approaches: one with an explicit inclusion of the CO molecule and one without. By comparing our simulations to existing experimental images, we ascribe the enhanced resolution of the CO functionalized tip to the special orbital characteristics of the CO molecule.

CO tip functionalization in subatomic resolution atomic force microscopy

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

Kim, Minjung; Chelikowsky, James R.

2015-10-19

Noncontact atomic force microscopy (nc-AFM) employing a CO-functionalized tip displays dramatically enhanced resolution wherein covalent bonds of polycyclic aromatic hydrocarbon can be imaged. Employing real-space pseudopotential first-principles calculations, we examine the role of CO in functionalizing the nc-AFM tip. Our calculations allow us to simulate full AFM images and ascertain the enhancement mechanism of the CO molecule. We consider two approaches: one with an explicit inclusion of the CO molecule and one without. By comparing our simulations to existing experimental images, we ascribe the enhanced resolution of the CO functionalized tip to the special orbital characteristics of the CO molecule.

A wireless centrifuge force microscope (CFM) enables multiplexed single-molecule experiments in a commercial centrifuge.

PubMed

Hoang, Tony; Patel, Dhruv S; Halvorsen, Ken

2016-08-01

The centrifuge force microscope (CFM) was recently introduced as a platform for massively parallel single-molecule manipulation and analysis. Here we developed a low-cost and self-contained CFM module that works directly within a commercial centrifuge, greatly improving accessibility and ease of use. Our instrument incorporates research grade video microscopy, a power source, a computer, and wireless transmission capability to simultaneously monitor many individually tethered microspheres. We validated the instrument by performing single-molecule force shearing of short DNA duplexes. For a 7 bp duplex, we observed over 1000 dissociation events due to force dependent shearing from 2 pN to 12 pN with dissociation times in the range of 10-100 s. We extended the measurement to a 10 bp duplex, applying a 12 pN force clamp and directly observing single-molecule dissociation over an 85 min experiment. Our new CFM module facilitates simple and inexpensive experiments that dramatically improve access to single-molecule analysis.

High resolution atomic force microscopy of double-stranded RNA.

PubMed

Ares, Pablo; Fuentes-Perez, Maria Eugenia; Herrero-Galán, Elías; Valpuesta, José M; Gil, Adriana; Gomez-Herrero, Julio; Moreno-Herrero, Fernando

2016-06-09

Double-stranded (ds) RNA mediates the suppression of specific gene expression, it is the genetic material of a number of viruses, and a key activator of the innate immune response against viral infections. The ever increasing list of roles played by dsRNA in the cell and its potential biotechnological applications over the last decade has raised an interest for the characterization of its mechanical properties and structure, and that includes approaches using Atomic Force Microscopy (AFM) and other single-molecule techniques. Recent reports have resolved the structure of dsDNA with AFM at unprecedented resolution. However, an equivalent study with dsRNA is still lacking. Here, we have visualized the double helix of dsRNA under near-physiological conditions and at sufficient resolution to resolve the A-form sub-helical pitch periodicity. We have employed different high-sensitive force-detection methods and obtained images with similar spatial resolution. Therefore, we show here that the limiting factors for high-resolution AFM imaging of soft materials in liquid medium are, rather than the imaging mode, the force between the tip and the sample and the sharpness of the tip apex.

Multiplexed single-molecule force spectroscopy using a centrifuge.

PubMed

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.

Multiplexed single-molecule force spectroscopy using a centrifuge

PubMed Central

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

2016-01-01

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. PMID:26984516

Stiffness, working stroke, and force of single-myosin molecules in skeletal muscle: elucidation of these mechanical properties via nonlinear elasticity evaluation.

PubMed

Kaya, Motoshi; Higuchi, Hideo

2013-11-01

In muscles, the arrays of skeletal myosin molecules interact with actin filaments and continuously generate force at various contraction speeds. Therefore, it is crucial for myosin molecules to generate force collectively and minimize the interference between individual myosin molecules. Knowledge of the elasticity of myosin molecules is crucial for understanding the molecular mechanisms of muscle contractions because elasticity directly affects the working and drag (resistance) force generation when myosin molecules are positively or negatively strained. The working stroke distance is also an important mechanical property necessary for elucidation of the thermodynamic efficiency of muscle contractions at the molecular level. In this review, we focus on these mechanical properties obtained from single-fiber and single-molecule studies and discuss recent findings associated with these mechanical properties. We also discuss the potential molecular mechanisms associated with reduction of the drag effect caused by negatively strained myosin molecules.

A comprehensive study of extended tetrathiafulvalene cruciform molecules for molecular electronics: synthesis and electrical transport measurements.

PubMed

Parker, Christian R; Leary, Edmund; Frisenda, Riccardo; Wei, Zhongming; Jennum, Karsten S; Glibstrup, Emil; Abrahamsen, Peter Bæch; Santella, Marco; Christensen, Mikkel A; Della Pia, Eduardo Antonio; Li, Tao; Gonzalez, Maria Teresa; Jiang, Xingbin; Morsing, Thorbjørn J; Rubio-Bollinger, Gabino; Laursen, Bo W; Nørgaard, Kasper; van der Zant, Herre; Agrait, Nicolas; Nielsen, Mogens Brøndsted

2014-11-26

Cruciform-like molecules with two orthogonally placed π-conjugated systems have in recent years attracted significant interest for their potential use as molecular wires in molecular electronics. Here we present synthetic protocols for a large selection of cruciform molecules based on oligo(phenyleneethynylene) (OPE) and tetrathiafulvalene (TTF) scaffolds, end-capped with acetyl-protected thiolates as electrode anchoring groups. The molecules were subjected to a comprehensive study of their conducting properties as well as their photophysical and electrochemical properties in solution. The complex nature of the molecules and their possible binding in different configurations in junctions called for different techniques of conductance measurements: (1) conducting-probe atomic force microscopy (CP-AFM) measurements on self-assembled monolayers (SAMs), (2) mechanically controlled break-junction (MCBJ) measurements, and (3) scanning tunneling microscopy break-junction (STM-BJ) measurements. The CP-AFM measurements showed structure-property relationships from SAMs of series of OPE3 and OPE5 cruciform molecules; the conductance of the SAM increased with the number of dithiafulvene (DTF) units (0, 1, 2) along the wire, and it increased when substituting two arylethynyl end groups of the OPE3 backbone with two DTF units. The MCBJ and STM-BJ studies on single molecules both showed that DTFs decreased the junction formation probability, but, in contrast, no significant influence on the single-molecule conductance was observed. We suggest that the origins of the difference between SAM and single-molecule measurements lie in the nature of the molecule-electrode interface as well as in effects arising from molecular packing in the SAMs. This comprehensive study shows that for complex molecules care should be taken when directly comparing single-molecule measurements and measurements of SAMs and solid-state devices thereof.

The Use of Atomic Force Microscopy for 3D Analysis of Nucleic Acid Hybridization on Microarrays.

PubMed

Dubrovin, E V; Presnova, G V; Rubtsova, M Yu; Egorov, A M; Grigorenko, V G; Yaminsky, I V

2015-01-01

Oligonucleotide microarrays are considered today to be one of the most efficient methods of gene diagnostics. The capability of atomic force microscopy (AFM) to characterize the three-dimensional morphology of single molecules on a surface allows one to use it as an effective tool for the 3D analysis of a microarray for the detection of nucleic acids. The high resolution of AFM offers ways to decrease the detection threshold of target DNA and increase the signal-to-noise ratio. In this work, we suggest an approach to the evaluation of the results of hybridization of gold nanoparticle-labeled nucleic acids on silicon microarrays based on an AFM analysis of the surface both in air and in liquid which takes into account of their three-dimensional structure. We suggest a quantitative measure of the hybridization results which is based on the fraction of the surface area occupied by the nanoparticles.

Atomic force microscopy – looking at mechanosensors on the cell surface

PubMed Central

Heinisch, Jürgen J.; Lipke, Peter N.; Beaussart, Audrey; El Kirat Chatel, Sofiane; Dupres, Vincent; Alsteens, David; Dufrêne, Yves F.

2012-01-01

Summary Living cells use cell surface proteins, such as mechanosensors, to constantly sense and respond to their environment. However, the way in which these proteins respond to mechanical stimuli and assemble into large complexes remains poorly understood at the molecular level. In the past years, atomic force microscopy (AFM) has revolutionized the way in which biologists analyze cell surface proteins to molecular resolution. In this Commentary, we discuss how the powerful set of advanced AFM techniques (e.g. live-cell imaging and single-molecule manipulation) can be integrated with the modern tools of molecular genetics (i.e. protein design) to study the localization and molecular elasticity of individual mechanosensors on the surface of living cells. Although we emphasize recent studies on cell surface proteins from yeasts, the techniques described are applicable to surface proteins from virtually all organisms, from bacteria to human cells. PMID:23077172

Magnetic tweezers for the measurement of twist and torque.

PubMed

Lipfert, Jan; Lee, Mina; Ordu, Orkide; Kerssemakers, Jacob W J; Dekker, Nynke H

2014-05-19

Single-molecule techniques make it possible to investigate the behavior of individual biological molecules in solution in real time. These techniques include so-called force spectroscopy approaches such as atomic force microscopy, optical tweezers, flow stretching, and magnetic tweezers. Amongst these approaches, magnetic tweezers have distinguished themselves by their ability to apply torque while maintaining a constant stretching force. Here, it is illustrated how such a "conventional" magnetic tweezers experimental configuration can, through a straightforward modification of its field configuration to minimize the magnitude of the transverse field, be adapted to measure the degree of twist in a biological molecule. The resulting configuration is termed the freely-orbiting magnetic tweezers. Additionally, it is shown how further modification of the field configuration can yield a transverse field with a magnitude intermediate between that of the "conventional" magnetic tweezers and the freely-orbiting magnetic tweezers, which makes it possible to directly measure the torque stored in a biological molecule. This configuration is termed the magnetic torque tweezers. The accompanying video explains in detail how the conversion of conventional magnetic tweezers into freely-orbiting magnetic tweezers and magnetic torque tweezers can be accomplished, and demonstrates the use of these techniques. These adaptations maintain all the strengths of conventional magnetic tweezers while greatly expanding the versatility of this powerful instrument.

Virtual reality visual feedback for hand-controlled scanning probe microscopy manipulation of single molecules.

PubMed

Leinen, Philipp; Green, Matthew F B; Esat, Taner; Wagner, Christian; Tautz, F Stefan; Temirov, Ruslan

2015-01-01

Controlled manipulation of single molecules is an important step towards the fabrication of single molecule devices and nanoscale molecular machines. Currently, scanning probe microscopy (SPM) is the only technique that facilitates direct imaging and manipulations of nanometer-sized molecular compounds on surfaces. The technique of hand-controlled manipulation (HCM) introduced recently in Beilstein J. Nanotechnol. 2014, 5, 1926-1932 simplifies the identification of successful manipulation protocols in situations when the interaction pattern of the manipulated molecule with its environment is not fully known. Here we present a further technical development that substantially improves the effectiveness of HCM. By adding Oculus Rift virtual reality goggles to our HCM set-up we provide the experimentalist with 3D visual feedback that displays the currently executed trajectory and the position of the SPM tip during manipulation in real time, while simultaneously plotting the experimentally measured frequency shift (Δf) of the non-contact atomic force microscope (NC-AFM) tuning fork sensor as well as the magnitude of the electric current (I) flowing between the tip and the surface. The advantages of the set-up are demonstrated by applying it to the model problem of the extraction of an individual PTCDA molecule from its hydrogen-bonded monolayer grown on Ag(111) surface.

Surface passivation for tight-binding calculations of covalent solids.

PubMed

Bernstein, N

2007-07-04

Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp(3) hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system.

Surface passivation for tight-binding calculations of covalent solids

NASA Astrophysics Data System (ADS)

Bernstein, N.

2007-07-01

Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp3 hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system.

High-speed atomic force microscopy coming of age

NASA Astrophysics Data System (ADS)

Ando, Toshio

2012-02-01

High-speed atomic force microscopy (HS-AFM) is now materialized. It allows direct visualization of dynamic structural changes and dynamic processes of functioning biological molecules in physiological solutions, at high spatiotemporal resolution. Dynamic molecular events unselectively appear in detail in an AFM movie, facilitating our understanding of how biological molecules operate to function. This review describes a historical overview of technical development towards HS-AFM, summarizes elementary devices and techniques used in the current HS-AFM, and then highlights recent imaging studies. Finally, future challenges of HS-AFM studies are briefly discussed.

Single molecule force spectroscopy reveals the adhesion mechanism of hydrophobins

NASA Astrophysics Data System (ADS)

Cao, Yi; Li, Bing; Qin, Meng; Wang, Wei

Hydrophobins are a special class of amphiphilic proteins produced by filamentous fungi. They show outstanding interfacial self-assembly and adhesion properties, which are critical to their biological function. Such feature also inspires their broad applications in bio-engineering, surface modification, and nanotechnology. However, the biophysical properties of hydrophobins are not well understood. We combined atomic force microscopy based single molecule force spectroscopy and protein engineering to directly quantify the adhesion strength of a hydorphobin (HFB1) to various surfaces in both the monomer and oligomer states to reveal the molecular determinant of the adhesion strength of hydrophobins. We found that the monomer HFB1 showed distinct adhesion properties towards hydrophobic and hydrophilic surfaces. The adhesion to hydrophobic surfaces (i.e. graphite and gold) was significantly higher than that to the hydrophilic ones (e.g. mica and silicon). However, when self-assembled monolayers were formed, the adhesion strengths to various surfaces were similar and were ubiquitously stronger than the monomer cases. We hypothesized that the interactions among hydrophobins in the monolayer played significant roles for the enhance adhesion strengths. Extracting any single hydrophobin monomers from the surface required the break of interactions not only with the surface but also with the neighboring units. We proposed that such a mechanism may be widely explored in nature for many biofilms for surface adhesion. May also inspire the design of novel adhesives.

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

Li, Mi; University of Chinese Academy of Sciences, Beijing 100049; Liu, Lianqing, E-mail: lqliu@sia.cn

Highlights: •Nanoscale cellular ultra-structures of macrophages were observed. •The binding affinities of FcγRs were measured directly on macrophages. •The nanoscale distributions of FcγRs were mapped on macrophages. -- Abstract: Fc gamma receptors (FcγR), widely expressed on effector cells (e.g., NK cells, macrophages), play an important role in clinical cancer immunotherapy. The binding of FcγRs to the Fc portions of antibodies that are attached to the target cells can activate the antibody-dependent cell-mediated cytotoxicity (ADCC) killing mechanism which leads to the lysis of target cells. In this work, we used atomic force microscopy (AFM) to observe the cellular ultra-structures and measuremore » the biophysical properties (affinity and distribution) of FcγRs on single macrophages in aqueous environments. AFM imaging was used to obtain the topographies of macrophages, revealing the nanoscale cellular fine structures. For molecular interaction recognition, antibody molecules were attached onto AFM tips via a heterobifunctional polyethylene glycol (PEG) crosslinker. With AFM single-molecule force spectroscopy, the binding affinities of FcγRs were quantitatively measured on single macrophages. Adhesion force mapping method was used to localize the FcγRs, revealing the nanoscale distribution of FcγRs on local areas of macrophages. The experimental results can improve our understanding of FcγRs on macrophages; the established approach will facilitate further research on physiological activities involved in antibody-based immunotherapy.« less

Alternative types of molecule-decorated atomic chains in Au–CO–Au single-molecule junctions

PubMed Central

Balogh, Zoltán; Makk, Péter

2015-01-01

Summary We investigate the formation and evolution of Au–CO single-molecule break junctions. The conductance histogram exhibits two distinct molecular configurations, which are further investigated by a combined statistical analysis. According to conditional histogram and correlation analysis these molecular configurations show strong anticorrelations with each other and with pure Au monoatomic junctions and atomic chains. We identify molecular precursor configurations with somewhat higher conductance, which are formed prior to single-molecule junctions. According to detailed length analysis two distinct types of molecule-affected chain-formation processes are observed, and we compare these results to former theoretical calculations considering bridge- and atop-type molecular configurations where the latter has reduced conductance due to destructive Fano interference. PMID:26199840

Alternative types of molecule-decorated atomic chains in Au-CO-Au single-molecule junctions.

PubMed

Balogh, Zoltán; Makk, Péter; Halbritter, András

2015-01-01

We investigate the formation and evolution of Au-CO single-molecule break junctions. The conductance histogram exhibits two distinct molecular configurations, which are further investigated by a combined statistical analysis. According to conditional histogram and correlation analysis these molecular configurations show strong anticorrelations with each other and with pure Au monoatomic junctions and atomic chains. We identify molecular precursor configurations with somewhat higher conductance, which are formed prior to single-molecule junctions. According to detailed length analysis two distinct types of molecule-affected chain-formation processes are observed, and we compare these results to former theoretical calculations considering bridge- and atop-type molecular configurations where the latter has reduced conductance due to destructive Fano interference.

Single Molecule Study of Force-Induced Rotation of Carbon-Carbon Double Bonds in Polymers.

PubMed

Huang, Wenmao; Zhu, Zhenshu; Wen, Jing; Wang, Xin; Qin, Meng; Cao, Yi; Ma, Haibo; Wang, Wei

2017-01-24

Carbon-carbon double bonds (C═C) are ubiquitous in natural and synthetic polymers. In bulk studies, due to limited ways to control applied force, they are thought to be mechanically inert and not to contribute to the extensibility of polymers. Here, we report a single molecule force spectroscopy study on a polymer containing C═C bonds using atomic force microscope. Surprisingly, we found that it is possible to directly observe the cis-to-trans isomerization of C═C bonds at the time scale of ∼1 ms at room temperature by applying a tensile force ∼1.7 nN. The reaction proceeds through a diradical intermediate state, as confirmed by both a free radical quenching experiment and quantum chemical modeling. The force-free activation length to convert the cis C═C bonds to the transition state is ∼0.5 Å, indicating that the reaction rate is accelerated by ∼10 9 times at the transition force. On the basis of the density functional theory optimized structure, we propose that because the pulling direction is not parallel to C═C double bonds in the polymer, stretching the polymer not only provides tension to lower the transition barrier but also provides torsion to facilitate the rotation of cis C═C bonds. This explains the apparently low transition force for such thermally "forbidden" reactions and offers an additional explanation of the "lever-arm effect" of polymer backbones on the activation force for many mechanophores. This work demonstrates the importance of precisely controlling the force direction at the nanoscale to the force-activated reactions and may have many implications on the design of stress-responsive materials.

A robust molecular probe for Ångstrom-scale analytics in liquids

PubMed Central

Nirmalraj, Peter; Thompson, Damien; Dimitrakopoulos, Christos; Gotsmann, Bernd; Dumcenco, Dumitru; Kis, Andras; Riel, Heike

2016-01-01

Traditionally, nanomaterial profiling using a single-molecule-terminated scanning probe is performed at the vacuum–solid interface often at a few Kelvin, but is not a notion immediately associated with liquid–solid interface at room temperature. Here, using a scanning tunnelling probe functionalized with a single C60 molecule stabilized in a high-density liquid, we resolve low-dimensional surface defects, atomic interfaces and capture Ångstrom-level bond-length variations in single-layer graphene and MoS2. Atom-by-atom controllable imaging contrast is demonstrated at room temperature and the electronic structure of the C60–metal probe complex within the encompassing liquid molecules is clarified using density functional theory. Our findings demonstrates that operating a robust single-molecular probe is not restricted to ultra-high vacuum and cryogenic settings. Hence the scope of high-precision analytics can be extended towards resolving sub-molecular features of organic elements and gauging ambient compatibility of emerging layered materials with atomic-scale sensitivity under experimentally less stringent conditions. PMID:27516157

Direct Single-Molecule Observation of Mode and Geometry of RecA-Mediated Homology Search.

PubMed

Lee, Andrew J; Endo, Masayuki; Hobbs, Jamie K; Wälti, Christoph

2018-01-23

Genomic integrity, when compromised by accrued DNA lesions, is maintained through efficient repair via homologous recombination. For this process the ubiquitous recombinase A (RecA), and its homologues such as the human Rad51, are of central importance, able to align and exchange homologous sequences within single-stranded and double-stranded DNA in order to swap out defective regions. Here, we directly observe the widely debated mechanism of RecA homology searching at a single-molecule level using high-speed atomic force microscopy (HS-AFM) in combination with tailored DNA origami frames to present the reaction targets in a way suitable for AFM-imaging. We show that RecA nucleoprotein filaments move along DNA substrates via short-distance facilitated diffusions, or slides, interspersed with longer-distance random moves, or hops. Importantly, from the specific interaction geometry, we find that the double-stranded substrate DNA resides in the secondary DNA binding-site within the RecA nucleoprotein filament helical groove during the homology search. This work demonstrates that tailored DNA origami, in conjunction with HS-AFM, can be employed to reveal directly conformational and geometrical information on dynamic protein-DNA interactions which was previously inaccessible at an individual single-molecule level.

High-speed atomic force microscopy for observing protein molecules in dynamic action

NASA Astrophysics Data System (ADS)

Ando, T.

2017-02-01

Directly observing protein molecules in dynamic action at high spatiotemporal resolution has long been a holy grail for biological science. To materialize this long quested dream, I have been developing high-speed atomic force microscopy (HS-AFM) since 1993. Tremendous strides were recently accomplished in its high-speed and low-invasive performances. Consequently, various dynamic molecular actions, including bipedal walking of myosin V and rotary propagation of structural changes in F1-ATPase, were successfully captured on video. The visualized dynamic images not only provided irrefutable evidence for speculated actions of the protein molecules but also brought new discoveries inaccessible with other approaches, thus giving great mechanistic insights into how the molecules function. HS-AFM is now transforming "static" structural biology into dynamic structural bioscience.

Microgravity

NASA Image and Video Library

2001-06-06

Atomic force microscopy uses laser technology to reveal a defect, a double-screw dislocation, on the surface of this crystal of canavalin, a major source of dietary protein for humans and domestic animals. When a crystal grows, attachment kinetics and transport kinetics are competing for control of the molecules. As a molecule gets close to the crystal surface, it has to attach properly for the crystal to be usable. NASA has funded investigators to look at those attachment kinetics from a theoretical standpoint and an experimental standpoint. Dr. Alex McPherson of the University of California, Irvine, is one of those investigators. He uses X-ray diffraction and atomic force microscopy in his laboratory to answer some of the many questions about how protein crystals grow. Atomic force microscopy provides a means of looking at how individual molecules are added to the surface of growing protein crystals. This helps McPherson understand the kinetics of protein crystal growth. McPherson asks, How fast do crystals grow? What are the forces involved? Investigators funded by NASA have clearly shown that such factors as the level of supersaturation and the rate of growth all affect the habit [characteristic arrangement of facets] of the crystal and the defects that occur in the crystal.

Protein crystal growth

NASA Technical Reports Server (NTRS)

2001-01-01

Atomic force microscopy uses laser technology to reveal a defect, a double-screw dislocation, on the surface of this crystal of canavalin, a major source of dietary protein for humans and domestic animals. When a crystal grows, attachment kinetics and transport kinetics are competing for control of the molecules. As a molecule gets close to the crystal surface, it has to attach properly for the crystal to be usable. NASA has funded investigators to look at those attachment kinetics from a theoretical standpoint and an experimental standpoint. Dr. Alex McPherson of the University of California, Irvine, is one of those investigators. He uses X-ray diffraction and atomic force microscopy in his laboratory to answer some of the many questions about how protein crystals grow. Atomic force microscopy provides a means of looking at how individual molecules are added to the surface of growing protein crystals. This helps McPherson understand the kinetics of protein crystal growth. McPherson asks, How fast do crystals grow? What are the forces involved? Investigators funded by NASA have clearly shown that such factors as the level of supersaturation and the rate of growth all affect the habit [characteristic arrangement of facets] of the crystal and the defects that occur in the crystal.

Depopulation of Single-Phthalocyanine Molecular Orbitals upon Pyrrolic-Hydrogen Abstraction on Graphene.

PubMed

Néel, Nicolas; Lattelais, Marie; Bocquet, Marie-Laure; Kröger, Jörg

2016-02-23

Single-molecule chemistry with a scanning tunneling microscope has preponderantly been performed on metal surfaces. The molecule-metal hybridization, however, is often detrimental to genuine molecular properties and obscures their changes upon chemical reactions. We used graphene on Ir(111) to reduce the coupling between Ir(111) and adsorbed phthalocyanine molecules. By local electron injection from the tip of a scanning tunneling microscope the two pyrrolic H atoms were removed from single phthalocyanines. The detachment of the H atom pair induced a strong modification of the molecular electronic structure, albeit with no change in the adsorption geometry. Spectra and maps of the differential conductance combined with density functional calculations unveiled the entire depopulation of the highest occupied molecular orbital upon H abstraction. Occupied π states of intact molecules are proposed to be emptied via intramolecular electron transfer to dangling σ states of H-free N atoms.

All-Atom MD Simulation of DNA Condensation Using Ab Initio Derived Force Field Parameters of Cobalt(III)-Hexammine.

PubMed

Sun, Tiedong; Mirzoev, Alexander; Korolev, Nikolay; Lyubartsev, Alexander P; Nordenskiöld, Lars

2017-08-24

It is well established that the presence of the trivalent cobalt(III)-hexammine cation (CoHex 3+ ) at submillimolar concentrations leads to bundling (condensation) of double-stranded DNA molecules, which is caused by DNA-DNA attraction induced by the multivalent counterions. However, the detailed mechanism of this process is still not fully understood. Furthermore, in all-atom molecular dynamics (MD) simulations, spontaneous aggregation of several DNA oligonucleotides in the presence of CoHex 3+ has previously not been demonstrated. In order to obtain a rigorous description of CoHex 3+ -nucleic acid interactions and CoHex 3+ -induced DNA condensation to be used in MD simulations, we have derived optimized force field parameters of the CoHex 3+ ion. They were obtained from Car-Parrinello molecular dynamics simulation of a single CoHex 3+ ion in the presence of 125 water molecules. The new set of force field parameters reproduces the experimentally known transition of DNA from B- to A-form, and qualitatively describes changes of DNA and RNA persistence lengths. We then carried out a 2 μs long atomistic simulation of four DNA oligomers each consisting of 36 base pairs in the presence of CoHex 3+ . We demonstrate that, in this system, DNA molecules display attractive interactions and aggregate into bundle-like structures. This behavior depends critically on the details of the CoHex 3+ interaction with DNA. A control simulation with a similar setup but in the presence of Mg 2+ does not induce DNA-DNA attraction, which is also in agreement with experiment.

Hydrogel Droplet Microfluidics for High-Throughput Single Molecule/Cell Analysis.

PubMed

Zhu, Zhi; Yang, Chaoyong James

2017-01-17

Heterogeneity among individual molecules and cells has posed significant challenges to traditional bulk assays, due to the assumption of average behavior, which would lose important biological information in heterogeneity and result in a misleading interpretation. Single molecule/cell analysis has become an important and emerging field in biological and biomedical research for insights into heterogeneity between large populations at high resolution. Compared with the ensemble bulk method, single molecule/cell analysis explores the information on time trajectories, conformational states, and interactions of individual molecules/cells, all key factors in the study of chemical and biological reaction pathways. Various powerful techniques have been developed for single molecule/cell analysis, including flow cytometry, atomic force microscopy, optical and magnetic tweezers, single-molecule fluorescence spectroscopy, and so forth. However, some of them have the low-throughput issue that has to analyze single molecules/cells one by one. Flow cytometry is a widely used high-throughput technique for single cell analysis but lacks the ability for intercellular interaction study and local environment control. Droplet microfluidics becomes attractive for single molecule/cell manipulation because single molecules/cells can be individually encased in monodisperse microdroplets, allowing high-throughput analysis and manipulation with precise control of the local environment. Moreover, hydrogels, cross-linked polymer networks that swell in the presence of water, have been introduced into droplet microfluidic systems as hydrogel droplet microfluidics. By replacing an aqueous phase with a monomer or polymer solution, hydrogel droplets can be generated on microfluidic chips for encapsulation of single molecules/cells according to the Poisson distribution. The sol-gel transition property endows the hydrogel droplets with new functionalities and diversified applications in single molecule/cell analysis. The hydrogel can act as a 3D cell culture matrix to mimic the extracellular environment for long-term single cell culture, which allows further heterogeneity study in proliferation, drug screening, and metastasis at the single-cell level. The sol-gel transition allows reactions in solution to be performed rapidly and efficiently with product storage in the gel for flexible downstream manipulation and analysis. More importantly, controllable sol-gel regulation provides a new way to maintain phenotype-genotype linkages in the hydrogel matrix for high throughput molecular evolution. In this Account, we will review the hydrogel droplet generation on microfluidics, single molecule/cell encapsulation in hydrogel droplets, as well as the progress made by our group and others in the application of hydrogel droplet microfluidics for single molecule/cell analysis, including single cell culture, single molecule/cell detection, single cell sequencing, and molecular evolution.

The formation of molecules in interstellar clouds from singly and multiply ionized atoms

NASA Technical Reports Server (NTRS)

Langer, W. D.

1978-01-01

The suggestion is considered that multiply ionized atoms produced by K- and L-shell X-ray ionization and cosmic-ray ionization can undergo ion-molecule reactions and also initiate molecule production. The role of X-rays in molecule production in general is discussed, and the contribution to molecule production of the C(+) radiative association with hydrogen is examined. Such gas-phase reactions of singly and multiply ionized atoms are used to calculate molecular abundances of carbon-, nitrogen-, and oxygen-bearing species. The column densities of the molecules are evaluated on the basis of a modified version of previously developed isobaric cloud models. It is found that reactions of multiply ionized carbon with H2 can contribute a significant fraction of the observed CH in diffuse interstellar clouds in the presence of diffuse X-ray structures or discrete X-ray sources and that substantial amounts of CH(+) can be produced under certain conditions.

Molecular vibrations in metal-single-molecule-metal junctions

NASA Astrophysics Data System (ADS)

Yokota, Kazumichi; Taniguchi, Masateru; Kawai, Tomoji

2010-03-01

Molecular vibrations in a metal-single-molecule-metal junction were studied based on density functional theory using a single benzenedithiolate molecule connected between gold clusters. We found that the difference in vibrational energy between an isolated benzenedithiol and the single-molecule junction is less than 3% in the energy range above 540 cm -1, where sulfur atoms contribute little to molecular vibrations. The finding implies that we can predict the peak energy in the inelastic electron tunneling spectrum of the single-molecule junction in the high energy range by vibrational analyses of isolated molecules.

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

PubMed

Sarkar, Ranja

2017-01-01

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

Forced unfolding of single-chain polymeric nanoparticles.

PubMed

Hosono, Nobuhiko; Kushner, Aaron M; Chung, Jaeyoon; Palmans, Anja R A; Guan, Zhibin; Meijer, E W

2015-06-03

Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is applied to single-chain polymeric nanoparticles (SCPNs) to acquire information about the internal folding structure of SCPNs and inherent kinetic parameters of supramolecular self-assembling motifs embedded into the SCPNs. The SCPNs used here are polyacrylate-based polymers carrying 2-ureido-4-[1H]-pyrimidinone (UPy) or benzene-1,3,5-tricarboxamide (BTA) pendants that induce an intramolecular chain collapse into nanoparticles consisting of one polymer chain only via internal supramolecular cross-linking. The SCPN is stretched by an AFM cantilever to unfold mechanically, which allows measuring of force-extension profiles of the SCPNs. Consecutive peaks observed in the force profiles are attributed to rupture events of self-assembled UPy/BTA units in the SCPNs. The force profiles have been analyzed statistically for a series of polymers with different UPy/BTA incorporation densities. The results provide insights into the internal conformation of SCPNs, where the folding structure can be changed with the incorporation density of UPy/BTA. In addition, dynamic loading rate analysis allows the determination of kinetic parameters of BTA self-assembly, which has not been accessible by any other method. This study offers a rational tool for understanding the folding structure, kinetics, and pathway of two series of SCPNs.

Resolving the molecular mechanism of cadherin catch bond formation

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

Manibog, Kristine; Li, Hui; Rakshit, Sabyasachi

2014-06-02

Classical cadherin Ca(2+)-dependent cell-cell adhesion proteins play key roles in embryogenesis and in maintaining tissue integrity. Cadherins mediate robust adhesion by binding in multiple conformations. One of these adhesive states, called an X-dimer, forms catch bonds that strengthen and become longer lived in the presence of mechanical force. Here we use single-molecule force-clamp spectroscopy with an atomic force microscope along with molecular dynamics and steered molecular dynamics simulations to resolve the molecular mechanisms underlying catch bond formation and the role of Ca(2+) ions in this process. Our data suggest that tensile force bends the cadherin extracellular region such that theymore » form long-lived, force-induced hydrogen bonds that lock X-dimers into tighter contact. When Ca(2+) concentration is decreased, fewer de novo hydrogen bonds are formed and catch bond formation is eliminated« less

Progressing single biomolecule force spectroscopy measurements for the screening of DNA binding agents

NASA Astrophysics Data System (ADS)

Zhang, Wenke; Barbagallo, Romina; Madden, Claire; Roberts, Clive J.; Woolford, Alison; Allen, Stephanie

2005-10-01

Recent studies have indicated that the force-extension properties of single molecules of double stranded (ds) DNA are sensitive to the presence of small molecule DNA binding agents, and also to their mode of binding. These observations raise the possibility of using this approach as a highly sensitive tool for the screening of such agents. However, particularly for studies employing the atomic force microscope (AFM), several non-trivial barriers hinder the progress of this approach to the non-specialist arena and hence also the full realization of this possibility. In this paper, we therefore address a series of key reproducibility and metrological issues associated with this type of measurement. Specifically, we present an improved immobilization method that covalently anchors one end (5' end) of a dual labelled (5'-thiol, 3'-biotin) p53 DNA molecule onto a gold substrate via gold-thiol chemistry, whilst the biotinylated 3' end is available for 'pick-up' using a streptavidin modified AFM tip. We also show that co-surface immobilization of DNA with 6-mercapto-1-hexanol (MCH) can also lead to a further increase the measured contour length. We demonstrate the impact of these improved protocols through the observation of the cooperative transition plateau in a DNA fragment of approximately 118 bp, a significantly smaller fragment than previously investigated. The results of a comparative study of the effects of a model minor groove binder (Hoechst 33258) and an intercalating drug (proflavine), alone, as a mixture and under different buffer conditions, are also presented.

Triple Helix Formation in a Topologically Controlled DNA Nanosystem.

PubMed

Yamagata, Yutaro; Emura, Tomoko; Hidaka, Kumi; Sugiyama, Hiroshi; Endo, Masayuki

2016-04-11

In the present study, we demonstrate single-molecule imaging of triple helix formation in DNA nanostructures. The binding of the single-molecule third strand to double-stranded DNA in a DNA origami frame was examined using two different types of triplet base pairs. The target DNA strand and the third strand were incorporated into the DNA frame, and the binding of the third strand was controlled by the formation of Watson-Crick base pairing. Triple helix formation was monitored by observing the structural changes in the incorporated DNA strands. It was also examined using a photocaged third strand wherein the binding of the third strand was directly observed using high-speed atomic force microscopy during photoirradiation. We found that the binding of the third strand could be controlled by regulating duplex formation and the uncaging of the photocaged strands in the designed nanospace. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Adhesion Forces between Lewis(X) Determinant Antigens as Measured by Atomic Force Microscopy.

PubMed

Tromas, C; Rojo, J; de la Fuente, J M; Barrientos, A G; García, R; Penadés, S

2001-01-01

The adhesion forces between individual molecules of Lewis(X) trisaccharide antigen (Le(X) ) have been measured in water and in calcium solution by using atomic force microscopy (AFM, see graph). These results demonstrate the self-recognition capability of this antigen, and reinforce the hypothesis that carbohydrate-carbohydrate interaction could be considered as the first step in the cell-adhesion process in nature. Copyright © 2001 WILEY-VCH Verlag GmbH, Weinheim, Fed. Rep. of Germany.

Electrospray deposition of organic molecules on bulk insulator surfaces.

PubMed

Hinaut, Antoine; Pawlak, Rémy; Meyer, Ernst; Glatzel, Thilo

2015-01-01

Large organic molecules are of important interest for organic-based devices such as hybrid photovoltaics or molecular electronics. Knowing their adsorption geometries and electronic structures allows to design and predict macroscopic device properties. Fundamental investigations in ultra-high vacuum (UHV) are thus mandatory to analyze and engineer processes in this prospects. With increasing size, complexity or chemical reactivity, depositing molecules by thermal evaporation becomes challenging. A recent way to deposit molecules in clean conditions is Electrospray Ionization (ESI). ESI keeps the possibility to work with large molecules, to introduce them in vacuum, and to deposit them on a large variety of surfaces. Here, ESI has been successfully applied to deposit triply fused porphyrin molecules on an insulating KBr(001) surface in UHV environment. Different deposition coverages have been obtained and characterization of the surface by in-situ atomic force microscopy working in the non-contact mode shows details of the molecular structures adsorbed on the surface. We show that UHV-ESI, can be performed on insulating surfaces in the sub-monolayer regime and to single molecules which opens the possibility to study a variety of complex molecules.

Ab initio simulations of subatomic resolution images in noncontact atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Minjung; Chelikowsky, James R.

2015-03-01

Direct imaging of polycyclic aromatic molecules with a subatomic resolution has recently been achieved with noncontact atomic force microscopy (nc-AFM). Specifically, nc-AFM employing a CO functionalized tip has provided details of the chemical bond in aromatic molecules, including the discrimination of bond order. However, the underlying physics of such high resolution imaging remains problematic. By employing new, efficient algorithms based on real space pseudopotentials, we calculate the forces between the nc-AFM tip and specimen. We simulate images of planar organic molecules with two different approaches: 1) with a chemically inert tip and 2) with a CO functionalized tip. We find dramatic differences in the resulting images, which are consistent with recent experimental work. Our work is supported by the DOE under DOE/DE-FG02-06ER46286 and by the Welch Foundation under Grant F-1837. Computational resources were provided by NERSC and XSEDE.

Consistent free energy landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation.

PubMed

Kim, Eunae; Jang, Soonmin; Pak, Youngshang

2007-10-14

We have attempted to improve the PARAM99 force field in conjunction with the generalized Born (GB) solvation model with a surface area correction for more consistent protein folding simulations. For this purpose, using an extended alphabeta training set of five well-studied molecules with various folds (alpha, beta, and betabetaalpha), a previously modified version of PARAM99/GBSA is further refined, such that all native states of the five training species correspond to their lowest free energy minimum states. The resulting modified force field (PARAM99MOD5/GBSA) clearly produces reasonably acceptable conformational free energy surfaces of the training set with correct identifications of their native states in the free energy minimum states. Moreover, due to its well-balanced nature, this new force field is expected to describe secondary structure propensities of diverse folds in a more consistent manner. Remarkably, temperature dependent behaviors simulated with the current force field are in good agreement with the experiment. This agreement is a significant improvement over the existing standard all-atom force fields. In addition, fundamentally important thermodynamic quantities, such as folding enthalpy (DeltaH) and entropy (DeltaS), agree reasonably well with the experimental data.

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

PubMed

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

2015-09-15

Although atomic force microscopy (AFM) was rapidly adopted as a routine surface imaging apparatus after its introduction in 1986, it has not been widely used in catalysis research. The reason is that common AFM operating modes do not provide the atomic resolution required to follow catalytic processes; rather the more complex noncontact (NC) mode is needed. Thus, scanning tunneling microscopy has been the principal tool for atomic scale catalysis research. In this Account, recent developments in NC-AFM will be presented that offer significant advantages for gaining a complete atomic level view of catalysis. The main advantage of NC-AFM is that the image contrast is due to the very short-range chemical forces that are of interest in catalysis. This motivated our development of 3D-AFM, a method that yields quantitative atomic resolution images of the potential energy surfaces that govern how molecules approach, stick, diffuse, and rebound from surfaces. A variation of 3D-AFM allows the determination of forces required to push atoms and molecules on surfaces, from which diffusion barriers and variations in adsorption strength may be obtained. Pushing molecules towards each other provides access to intermolecular interaction between reaction partners. Following reaction, NC-AFM with CO-terminated tips yields textbook images of intramolecular structure that can be used to identify reaction intermediates and products. Because NC-AFM and STM contrast mechanisms are distinct, combining the two methods can produce unique insight. It is demonstrated for surface-oxidized Cu(100) that simultaneous 3D-AFM/STM yields resolution of both the Cu and O atoms. Moreover, atomic defects in the Cu sublattice lead to variations in the reactivity of the neighboring O atoms. It is shown that NC-AFM also allows a straightforward imaging of work function variations which has been used to identify defect charge states on catalytic surfaces and to map charge transfer within an individual molecule. These advances highlight the potential for NC-AFM-based methods to become the cornerstone upon which a quantitative atomic scale view of each step of a catalytic process may be gained. Realizing this potential will rely on two breakthroughs: (1) development of robust methods for tip functionalization and (2) simplification of NC-AFM instrumentation and control schemes. Quartz force sensors may offer paths forward in both cases. They allow any material with an atomic asperity to be used as a tip, opening the door to a wide range of surface functionalization chemistry. In addition, they do not suffer from the instabilities that motivated the initial adoption of complex control strategies that are still used today.

Conformational Smear Characterization and Binning of Single-Molecule Conductance Measurements for Enhanced Molecular Recognition.

PubMed

Korshoj, Lee E; Afsari, Sepideh; Chatterjee, Anushree; Nagpal, Prashant

2017-11-01

Electronic conduction or charge transport through single molecules depends primarily on molecular structure and anchoring groups and forms the basis for a wide range of studies from molecular electronics to DNA sequencing. Several high-throughput nanoelectronic methods such as mechanical break junctions, nanopores, conductive atomic force microscopy, scanning tunneling break junctions, and static nanoscale electrodes are often used for measuring single-molecule conductance. In these measurements, "smearing" due to conformational changes and other entropic factors leads to large variances in the observed molecular conductance, especially in individual measurements. Here, we show a method for characterizing smear in single-molecule conductance measurements and demonstrate how binning measurements according to smear can significantly enhance the use of individual conductance measurements for molecular recognition. Using quantum point contact measurements on single nucleotides within DNA macromolecules, we demonstrate that the distance over which molecular junctions are maintained is a measure of smear, and the resulting variance in unbiased single measurements depends on this smear parameter. Our ability to identify individual DNA nucleotides at 20× coverage increases from 81.3% accuracy without smear analysis to 93.9% with smear characterization and binning (SCRIB). Furthermore, merely 7 conductance measurements (7× coverage) are needed to achieve 97.8% accuracy for DNA nucleotide recognition when only low molecular smear measurements are used, which represents a significant improvement over contemporary sequencing methods. These results have important implications in a broad range of molecular electronics applications from designing robust molecular switches to nanoelectronic DNA sequencing.

Epitaxially Grown Films of Standing and Lying Pentacene Molecules on Cu(110) Surfaces

PubMed Central

2011-01-01

Here, it is shown that pentacene thin films (30 nm) with distinctively different crystallographic structures and molecular orientations can be grown under essentially identical growth conditions in UHV on clean Cu(110) surfaces. By X-ray diffraction, we show that the epitaxially oriented pentacene films crystallize either in the “thin film” phase with standing molecules or in the “single crystal” structure with molecules lying with their long axes parallel to the substrate. The morphology of the samples observed by atomic force microscopy shows an epitaxial alignment of pentacene crystallites, which corroborates the molecular orientation observed by X-ray diffraction pole figures. Low energy electron diffraction measurements reveal that these dissimilar growth behaviors are induced by subtle differences in the monolayer structures formed by slightly different preparation procedures. PMID:21479111

Crystallinity of the epitaxial heterojunction of C60 on single crystal pentacene

NASA Astrophysics Data System (ADS)

Tsuruta, Ryohei; Mizuno, Yuta; Hosokai, Takuya; Koganezawa, Tomoyuki; Ishii, Hisao; Nakayama, Yasuo

2017-06-01

The structure of pn heterojunctions is an important subject in the field of organic semiconductor devices. In this work, the crystallinity of an epitaxial pn heterojunction of C60 on single crystal pentacene is investigated by non-contact mode atomic force microscopy and high-resolution grazing incidence x-ray diffraction. Analysis shows that the C60 molecules assemble into grains consisting of single crystallites on the pentacene single crystal surface. The in-plane mean crystallite size exceeds 0.1 μm, which is at least five time larger than the size of crystallites deposited onto polycrystalline pentacene thin films grown on SiO2. The results indicate that improvement in the crystal quality of the underlying molecular substrate leads to drastic promotion of the crystallinity at the organic semiconductor heterojunction.

A single-molecule force spectroscopy study of the interactions between lectins and carbohydrates on cancer and normal cells

NASA Astrophysics Data System (ADS)

Zhao, Weidong; Cai, Mingjun; Xu, Haijiao; Jiang, Junguang; Wang, Hongda

2013-03-01

The interaction forces between carbohydrates and lectins were investigated by single-molecule force spectroscopy on both cancer and normal cells. The binding kinetics was also studied, which shows that the carbohydrate-lectin complex on cancer cells is less stable than that on normal cells.The interaction forces between carbohydrates and lectins were investigated by single-molecule force spectroscopy on both cancer and normal cells. The binding kinetics was also studied, which shows that the carbohydrate-lectin complex on cancer cells is less stable than that on normal cells. Electronic supplementary information (ESI) available: Experimental details. See DOI: 10.1039/c3nr00553d

Simple horizontal magnetic tweezers for micromanipulation of single DNA molecules and DNA–protein complexes

PubMed Central

McAndrew, Christopher P.; Tyson, Christopher; Zischkau, Joseph; Mehl, Patrick; Tuma, Pamela L.; Pegg, Ian L.; Sarkar, Abhijit

2016-01-01

We report the development of a simple-to-implement magnetic force transducer that can apply a wide range of piconewton (pN) scale forces on single DNA molecules and DNA–protein complexes in the horizontal plane. The resulting low-noise force-extension data enable very high-resolution detection of changes in the DNA tether’s extension: ~0.05 pN in force and <10 nm change in extension. We have also verified that we can manipulate DNA in near equilibrium conditions through the wide range of forces by ramping the force from low to high and back again, and observing minimal hysteresis in the molecule’s force response. Using a calibration technique based on Stokes’ drag law, we have confirmed our force measurements from DNA force-extension experiments obtained using the fluctuation-dissipation theorem applied to transverse fluctuations of the magnetic microsphere. We present data on the force-distance characteristics of a DNA molecule complexed with histones. The results illustrate how the tweezers can be used to study DNA binding proteins at the single molecule level. PMID:26757808

Ground Based Program for the Physical Analysis of Macromolecular Crystal Growth

NASA Technical Reports Server (NTRS)

Malkin, Alexander J.

1998-01-01

During the past year we have focused on application of in situ Atomic Force Microscopy (AFM) for studies of the growth mechanisms and kinetics of crystallization for different macromolecular systems. Mechanisms of macrostep formation and their decay, which are important in understanding of defect formation, were studied on the surfaces of thaumatin, catalase, canavalin and lysozyme crystals. Experiments revealed that step bunching on crystalline surfaces occurred either due to two- or three-dimensional nucleation on the terraces of vicinal slopes or as a result of uneven step generation by complex dislocation sources. No step bunching arising from interaction of individual steps in the course of the experiment was observed. The molecular structure of the growth steps for thaumatin and lipase crystals were deduced. It was further shown that growth step advance occurs by incorporation of single protein molecules. In singular directions growth steps move by one-dimensional nucleation on step edges followed by lateral growth. One-dimensional nuclei have different sizes, less then a single unit cell, varying for different directions of step movement. There is no roughness due to thermal fluctuations, and each protein molecule which incorporated into the step remained. Growth kinetics for catalase crystals was investigated over wide supersaturation ranges. Strong directional kinetic anisotropy in the tangential step growth rates in different directions was seen. The influence of impurities on growth kinetics and cessation of macromolecular crystals was studied. Thus, for catalase, in addition to pronounced impurity effects on the kinetics of crystallization, we were also able to directly observe adsorption of some impurities. At low supersaturation we repeatedly observed filaments which formed from impurity molecules sedimenting on the surfaces. Similar filaments were observed on the surfaces of thaumatin, canavalin and STMV crystals as well, but the frequency was low compared with catalase crystallization. Cessation of growth of xylanase and lysozyme crystals was also observed and appeared to be a consequence of the formation of dense impurity adsorption layers. Attachment: "An in situ AFM investigation of catalase crystallization", "Atomic force microscopy studies of living cells: visualization of motility, division, aggregation, transformation, and apoptosis", AFM studies on mechanisms of nucleation and growth of macromolecular crystals", and "In situ atomic force microscopy studies of surface morphology, growth kinetics, defect structure and dissolution in macromolecular crystallization".

Numerical Study on the Partitioning of the Molecular Polarizability into Fluctuating Charge and Induced Atomic Dipole Contributions

PubMed Central

Mei, Ye; Simmonett, Andrew C.; Pickard, Frank C.; DiStasio, Robert A.; Brooks, Bernard R.; Shao, Yihan

2015-01-01

In order to carry out a detailed analysis of the molecular static polarizability, which is the response of the molecule to a uniform external electric field, the molecular polarizability was computed using the finite-difference method for 21 small molecules, using density functional theory. Within nine charge population schemes (Löwdin, Mulliken, Becke, Hirshfeld, CM5, Hirshfeld-I, NPA, CHELPG, MK-ESP) in common use, the charge fluctuation contribution is found to dominate the molecular polarizability, with its ratio ranging from 59.9% with the Hirshfeld or CM5 scheme to 96.2% with the Mulliken scheme. The Hirshfeld-I scheme is also used to compute the other contribution to the molecular polarizability coming from the induced atomic dipoles, and the atomic polarizabilities in 8 small molecules and water pentamer are found to be highly anisotropic for most atoms. Overall, the results suggest that (a) more emphasis probably should be placed on the charge fluctuation terms in future polarizable force field development; (b) an anisotropic polarizability might be more suitable than an isotropic one in polarizable force fields based entirely or partially on the induced atomic dipoles. PMID:25945749

Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions

DOE PAGES

Mei, Ye; Simmonett, Andrew C.; Pickard, IV, Frank C.; ...

2015-05-06

In order to carry out a detailed analysis of the molecular static polarizability, which is the response of the molecule to a uniform external electric field, the molecular polarizability was computed in this study using the finite-difference method for 21 small molecules, using density functional theory. Within nine charge population schemes (Lowdin, Mulliken, Becke, Hirshfeld, CM5, Hirshfeld-I, NPA, CHELPG, MK-ESP) in common use, the charge fluctuation contribution is found to dominate the molecular polarizability, with its ratio ranging from 59.9% with the Hirshfeld or CM5 scheme to 96.2% with the Mulliken scheme. The Hirshfeld-I scheme is also used to computemore » the other contribution to the molecular polarizability coming from the induced atomic dipoles, and the atomic polarizabilities in eight small molecules and water pentamer are found to be highly anisotropic for most atoms. In conclusion, the overall results suggest that (a) more emphasis probably should be placed on the charge fluctuation terms in future polarizable force field development and (b) an anisotropic polarizability might be more suitable than an isotropic one in polarizable force fields based entirely or partially on the induced atomic dipoles.« less

Quantifying the atomic-level mechanics of single long physisorbed molecular chains.

PubMed

Kawai, Shigeki; Koch, Matthias; Gnecco, Enrico; Sadeghi, Ali; Pawlak, Rémy; Glatzel, Thilo; Schwarz, Jutta; Goedecker, Stefan; Hecht, Stefan; Baratoff, Alexis; Grill, Leonhard; Meyer, Ernst

2014-03-18

Individual in situ polymerized fluorene chains 10-100 nm long linked by C-C bonds are pulled vertically from an Au(111) substrate by the tip of a low-temperature atomic force microscope. The conformation of the selected chains is imaged before and after manipulation using scanning tunneling microscopy. The measured force gradient shows strong and periodic variations that correspond to the step-by-step detachment of individual fluorene repeat units. These variations persist at constant intensity until the entire polymer is completely removed from the surface. Calculations based on an extended Frenkel-Kontorova model reproduce the periodicity and magnitude of these features and allow us to relate them to the detachment force and desorption energy of the repeat units. The adsorbed part of the polymer slides easily along the surface during the pulling process, leading to only small oscillations as a result of the high stiffness of the fluorenes and of their length mismatch with respect to the substrate surface structure. A significant lateral force also is caused by the sequential detachment of individual units. The gained insight into the molecule-surface interactions during sliding and pulling should aid the design of mechanoresponsive nanosystems and devices.

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

PubMed

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

2010-01-01

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

Substitution Structures of Large Molecules and Medium Range Correlations in Quantum Chemistry Calculations

NASA Astrophysics Data System (ADS)

Evangelisti, Luca; Pate, Brooks

2017-06-01

A study of the minimally exciting topic of agreement between experimental and measured rotational constants of molecules was performed on a set of large molecules with 16-18 heavy atoms (carbon and oxygen). The molecules are: nootkatone (C_{15}H_{22}O), cedrol (C_{15}H_{26}O), ambroxide (C_{16}H_{28}O), sclareolide (C_{16}H_{22}O_{2}), and dihydroartemisinic acid (C_{15}H_{24}O_{2}). For this set of molecules we obtained 13C-subsitution structures for six molecules (this includes two conformers of nootkatone). A comparison of theoretical structures and experimental substitution structures was performed in the spirit of the recent work of Grimme and Steinmetz.[1] Our analysis focused the center-of-mass distance of the carbon atoms in the molecules. Four different computational methods were studied: standard DFT (B3LYP), dispersion corrected DFT (B3LYP-D3BJ), hybrid DFT with dispersion correction (B2PLYP-D3), and MP2. A significant difference in these theories is how they handle medium range correlation of electrons that produce dispersion forces. For larger molecules, these dispersion forces produce an overall contraction of the molecule around the center-of-mass. DFT poorly treats this effect and produces structures that are too expanded. MP2 calculations overestimate the correction and produce structures that are too compact. Both dispersion corrected DFT methods produce structures in excellent agreement with experiment. The analysis shows that the difference in computational methods can be described by a linear error in the center-of-mass distance. This makes it possible to correct poorer performing calculations with a single scale factor. We also reexamine the issue of the "Costain error" in substitution structures and show that it is significantly larger in these systems than in the smaller molecules used by Costain to establish the error limits. [1] Stefan Grimme and Marc Steinmetz, "Effects of London dispersion correction in density functional theory on structures of organic molecules in the gas phase", Phys. Chem. Chem. Phys. 15, 16031-16042 (2013).

Ordered Self-Assembled Monolayers of Peptide Nucleic Acids with DNA Recognition Capability

NASA Astrophysics Data System (ADS)

Briones, C.; Mateo-Marti, E.; Gómez-Navarro, C.; Parro, V.; Román, E.; Martín-Gago, J. A.

2004-11-01

We report on the formation of ordered self-assembled monolayers (SAMs) of single-stranded peptide nucleic acids (ssPNA). In spite of their remarkable length (7nm) thiolated PNAs assemble standing up on gold surfaces similarly to the SAMs of short alkanethiols. SAMs of ssPNA recognize complementary nucleic acids, acting as specific biosensors that discriminate even a point mutation in target ssDNA. These results are obtained by surface characterization techniques that avoid labeling of the target molecule: x-ray photoemission, x-ray absorption and atomic force microscopy.

Toward a detailed description of the pathways of allosteric communication in the GroEL chaperonin through atomistic simulation.

PubMed

Piggot, Thomas J; Sessions, Richard B; Burston, Steven G

2012-02-28

GroEL, along with its coprotein GroES, is essential for ensuring the correct folding of unfolded or newly synthesized proteins in bacteria. GroEL is a complex, allosteric molecule, composed of two heptameric rings stacked back to back, that undergoes large structural changes during its reaction cycle. These structural changes are driven by the cooperative binding and subsequent hydrolysis of ATP, by GroEL. Despite numerous previous studies, the precise mechanisms of allosteric communication and the associated structural changes remain elusive. In this paper, we describe a series of all-atom, unbiased, molecular dynamics simulations over relatively long (50-100 ns) time scales of a single, isolated GroEL subunit and also a heptameric GroEL ring, in the presence and absence of ATP. Combined with results from a distance restraint-biased simulation of the single ring, the atomistic details of the earliest stages of ATP-driven structural changes within this complex molecule are illuminated. Our results are in broad agreement with previous modeling studies of isolated subunits and with a coarse-grained, forcing simulation of the single ring. These are the first reported all-atom simulations of the GroEL single-ring complex and provide a unique insight into the role of charged residues K80, K277, R284, R285, and E388 at the subunit interface in transmission of the allosteric signal. These simulations also demonstrate the feasibility of performing all-atom simulations of very large systems on sufficiently long time scales on typical high performance computing facilities to show the origins of the earliest events in biologically relevant processes.

Force Spectroscopy with 9-μs Resolution and Sub-pN Stability by Tailoring AFM Cantilever Geometry.

PubMed

Edwards, Devin T; Faulk, Jaevyn K; LeBlanc, Marc-André; Perkins, Thomas T

2017-12-19

Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is a powerful yet accessible means to characterize the unfolding/refolding dynamics of individual molecules and resolve closely spaced, transiently occupied folding intermediates. On a modern commercial AFM, these applications and others are now limited by the mechanical properties of the cantilever. Specifically, AFM-based SMFS data quality is degraded by a commercial cantilever's limited combination of temporal resolution, force precision, and force stability. Recently, we modified commercial cantilevers with a focused ion beam to optimize their properties for SMFS. Here, we extend this capability by modifying a 40 × 18 μm 2 cantilever into one terminated with a gold-coated, 4 × 4 μm 2 reflective region connected to an uncoated 2-μm-wide central shaft. This "Warhammer" geometry achieved 8.5-μs resolution coupled with improved force precision and sub-pN stability over 100 s when measured on a commercial AFM. We highlighted this cantilever's biological utility by first resolving a calmodulin unfolding intermediate previously undetected by AFM and then measuring the stabilization of calmodulin by myosin light chain kinase at dramatically higher unfolding velocities than in previous AFM studies. More generally, enhancing data quality via an improved combination of time resolution, force precision, and force stability will broadly benefit biological applications of AFM. Published by Elsevier Inc.

Tip-Enhanced Raman Voltammetry: Coverage Dependence and Quantitative Modeling.

PubMed

Mattei, Michael; Kang, Gyeongwon; Goubert, Guillaume; Chulhai, Dhabih V; Schatz, George C; Jensen, Lasse; Van Duyne, Richard P

2017-01-11

Electrochemical atomic force microscopy tip-enhanced Raman spectroscopy (EC-AFM-TERS) was employed for the first time to observe nanoscale spatial variations in the formal potential, E 0' , of a surface-bound redox couple. TERS cyclic voltammograms (TERS CVs) of single Nile Blue (NB) molecules were acquired at different locations spaced 5-10 nm apart on an indium tin oxide (ITO) electrode. Analysis of TERS CVs at different coverages was used to verify the observation of single-molecule electrochemistry. The resulting TERS CVs were fit to the Laviron model for surface-bound electroactive species to quantitatively extract the formal potential E 0' at each spatial location. Histograms of single-molecule E 0' at each coverage indicate that the electrochemical behavior of the cationic oxidized species is less sensitive to local environment than the neutral reduced species. This information is not accessible using purely electrochemical methods or ensemble spectroelectrochemical measurements. We anticipate that quantitative modeling and measurement of site-specific electrochemistry with EC-AFM-TERS will have a profound impact on our understanding of the role of nanoscale electrode heterogeneity in applications such as electrocatalysis, biological electron transfer, and energy production and storage.

Hands-on Force Spectroscopy: Weird Springs and Protein Folding

ERIC Educational Resources Information Center

Euler, Manfred

2008-01-01

A force spectroscopy model experiment is presented using a low-cost tensile apparatus described earlier. Force-extension measurements of twisted rubber bands are obtained. They exhibit a complex nonlinear elastic behaviour that resembles atomic force spectroscopy investigations of molecules of titin, a muscle protein. The model experiments open up…

Zero-phonon-line emission of single molecules for applications in quantum information processing

NASA Astrophysics Data System (ADS)

Kiraz, Alper; Ehrl, M.; Mustecaplioglu, O. E.; Hellerer, T.; Brauchle, C.; Zumbusch, A.

2005-07-01

A single photon source which generates transform limited single photons is highly desirable for applications in quantum optics. Transform limited emission guarantees the indistinguishability of the emitted single photons. This, in turn brings groundbreaking applications in linear optics quantum information processing within an experimental reach. Recently, self-assembled InAs quantum dots and trapped atoms have successfully been demonstrated as such sources for highly indistinguishable single photons. Here, we demonstrate that nearly transform limited zero-phonon-line (ZPL) emission from single molecules can be obtained by using vibronic excitation. Furthermore we report the results of coincidence detection experiments at the output of a Michelson-type interferometer. These experiments reveal Hong-Ou-Mandel correlations as a proof of the indistinguishability of the single photons emitted consecutively from a single molecule. Therefore, single molecules constitute an attractive alternative to single InAs quantum dots and trapped atoms for applications in linear optics quantum information processing. Experiments were performed with a home-built confocal microscope keeping the sample in a superfluid liquid Helium bath at 1.4K. We investigated terrylenediimide (TDI) molecules highly diluted in hexadecane (Shpol'skii matrix). A continuous wave single mode dye laser was used for excitation of vibronic transitions of individual molecules. From the integral fluorescence, the ZPL of single molecules was selected with a spectrally narrow interference filter. The ZPL emission was then sent to a scanning Fabry-Perot interferometer for linewidth measurements or a Michelson-type interferometer for coincidence detection.

High-Speed Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Ando, Toshio; Uchihashi, Takayuki; Kodera, Noriyuki

2012-08-01

The technology of high-speed atomic force microscopy (HS-AFM) has reached maturity. HS-AFM enables us to directly visualize the structure and dynamics of biological molecules in physiological solutions at subsecond to sub-100 ms temporal resolution. By this microscopy, dynamically acting molecules such as myosin V walking on an actin filament and bacteriorhodopsin in response to light are successfully visualized. High-resolution molecular movies reveal the dynamic behavior of molecules in action in great detail. Inferences no longer have to be made from static snapshots of molecular structures and from the dynamic behavior of optical markers attached to biomolecules. In this review, we first describe theoretical considerations for the highest possible imaging rate, then summarize techniques involved in HS-AFM and highlight recent imaging studies. Finally, we briefly discuss future challenges to explore.

Collision events between RNA polymerases in convergent transcription studied by atomic force microscopy

PubMed Central

Crampton, Neal; Bonass, William A.; Kirkham, Jennifer; Rivetti, Claudio; Thomson, Neil H.

2006-01-01

Atomic force microscopy (AFM) has been used to image, at single molecule resolution, transcription events by Escherichia coli RNA polymerase (RNAP) on a linear DNA template with two convergently aligned λpr promoters. For the first time experimentally, the outcome of collision events during convergent transcription by two identical RNAP has been studied. Measurement of the positions of the RNAP on the DNA, allows distinction of open promoter complexes (OPCs) and elongating complexes (EC) and collided complexes (CC). This discontinuous time-course enables subsequent analysis of collision events where both RNAP remain bound on the DNA. After collision, the elongating RNAP has caused the other (usually stalled) RNAP to back-track along the template. The final positions of the two RNAP indicate that these are collisions between an EC and a stalled EC (SEC) or OPC (previously referred to as sitting-ducks). Interestingly, the distances between the two RNAP show that they are not always at closest approach after ‘collision’ has caused their arrest. PMID:17012275

Single-Cell Force Spectroscopy of Probiotic Bacteria

PubMed Central

Beaussart, Audrey; El-Kirat-Chatel, Sofiane; Herman, Philippe; Alsteens, David; Mahillon, Jacques; Hols, Pascal; Dufrêne, Yves F.

2013-01-01

Single-cell force spectroscopy is a powerful atomic force microscopy modality in which a single living cell is attached to the atomic force microscopy cantilever to quantify the forces that drive cell-cell and cell-substrate interactions. Although various single-cell force spectroscopy protocols are well established for animal cells, application of the method to individual bacterial cells remains challenging, mainly owing to the lack of appropriate methods for the controlled attachment of single live cells on cantilevers. We present a nondestructive protocol for single-bacterial cell force spectroscopy, which combines the use of colloidal probe cantilevers and of a bioinspired polydopamine wet adhesive. Living cells from the probiotic species Lactobacillus plantarum are picked up with a polydopamine-coated colloidal probe, enabling us to quantify the adhesion forces between single bacteria and biotic (lectin monolayer) or abiotic (hydrophobic monolayer) surfaces. These minimally invasive single-cell experiments provide novel, to our knowledge, insight into the specific and nonspecific forces driving the adhesion of L. plantarum, and represent a generic platform for studying the molecular mechanisms of cell adhesion in probiotic and pathogenic bacteria. PMID:23663831

Nanofabrication technique based on localized photocatalytic reactions using a TiO2-coated atomic force microscopy probe

NASA Astrophysics Data System (ADS)

Shibata, Takayuki; Iio, Naohiro; Furukawa, Hiromi; Nagai, Moeto

2017-02-01

We performed a fundamental study on the photocatalytic degradation of fluorescently labeled DNA molecules immobilized on titanium dioxide (TiO2) thin films under ultraviolet irradiation. The films were prepared by the electrochemical anodization of Ti thin films sputtered on silicon substrates. We also confirmed that the photocurrent arising from the photocatalytic oxidation of DNA molecules can be detected during this process. We then demonstrated an atomic force microscopy (AFM)-based nanofabrication technique by employing TiO2-coated AFM probes to penetrate living cell membranes under near-physiological conditions for minimally invasive intracellular delivery.

Single molecule views of Nature's nano-machines

NASA Astrophysics Data System (ADS)

Ha, Taekjip

2006-03-01

We are interested in the perturbational analysis of biological molecules to better understand their mechanisms. Our readout is the fluorescence signal from individual biomolecules, mainly in the form of single molecule fluorescence resonance energy transfer (FRET). We are pioneering approaches to perturb and control biomolecular conformations using external force (combination of single molecule FRET and optical trap) or other biological motifs (DNA hybridization, G-quadruplex, aptamers,.). In this talk, I will present our latest results on mapping the conformational energy landscape of the Holliday junction through simultaneous fluorescence and force measurements. In addition, a new nanomechanical device called single molecule nano-metronome will be discussed with an outlook toward controlling protein conformations using nucleic acids motifs.

1,3,5-trinitro-1,3,5-triazine decomposition and chemisorption on Al(111) surface: first-principles molecular dynamics study.

PubMed

Umezawa, Naoto; Kalia, Rajiv K; Nakano, Aiichiro; Vashista, Priya; Shimojo, Fuyuki

2007-06-21

We have investigated the decomposition and chemisorption of a 1,3,5-trinitro-1,3,5-triazine (RDX) molecule on Al(111) surface using molecular dynamics simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory (DFT). The real-space DFT calculations are based on higher-order finite difference and norm-conserving pseudopotential methods. Strong attractive forces between oxygen and aluminum atoms break N-O and N-N bonds in the RDX and, subsequently, the dissociated oxygen atoms and NO molecules oxidize the Al surface. In addition to these Al surface-assisted decompositions, ring cleavage of the RDX molecule is also observed. These reactions occur spontaneously without potential barriers and result in the attachment of the rest of the RDX molecule to the surface. This opens up the possibility of coating Al nanoparticles with RDX molecules to avoid the detrimental effect of oxidation in high energy density material applications.

Harmonic force spectroscopy measures load-dependent kinetics of individual human β-cardiac myosin molecules.

PubMed

Sung, Jongmin; Nag, Suman; Mortensen, Kim I; Vestergaard, Christian L; Sutton, Shirley; Ruppel, Kathleen; Flyvbjerg, Henrik; Spudich, James A

2015-08-04

Molecular motors are responsible for numerous cellular processes from cargo transport to heart contraction. Their interactions with other cellular components are often transient and exhibit kinetics that depend on load. Here, we measure such interactions using 'harmonic force spectroscopy'. In this method, harmonic oscillation of the sample stage of a laser trap immediately, automatically and randomly applies sinusoidally varying loads to a single motor molecule interacting with a single track along which it moves. The experimental protocol and the data analysis are simple, fast and efficient. The protocol accumulates statistics fast enough to deliver single-molecule results from single-molecule experiments. We demonstrate the method's performance by measuring the force-dependent kinetics of individual human β-cardiac myosin molecules interacting with an actin filament at physiological ATP concentration. We show that a molecule's ADP release rate depends exponentially on the applied load, in qualitative agreement with cardiac muscle, which contracts with a velocity inversely proportional to external load.

Harmonic force spectroscopy measures load-dependent kinetics of individual human β-cardiac myosin molecules

PubMed Central

Sung, Jongmin; Nag, Suman; Mortensen, Kim I.; Vestergaard, Christian L.; Sutton, Shirley; Ruppel, Kathleen; Flyvbjerg, Henrik; Spudich, James A.

2015-01-01

Molecular motors are responsible for numerous cellular processes from cargo transport to heart contraction. Their interactions with other cellular components are often transient and exhibit kinetics that depend on load. Here, we measure such interactions using ‘harmonic force spectroscopy'. In this method, harmonic oscillation of the sample stage of a laser trap immediately, automatically and randomly applies sinusoidally varying loads to a single motor molecule interacting with a single track along which it moves. The experimental protocol and the data analysis are simple, fast and efficient. The protocol accumulates statistics fast enough to deliver single-molecule results from single-molecule experiments. We demonstrate the method's performance by measuring the force-dependent kinetics of individual human β-cardiac myosin molecules interacting with an actin filament at physiological ATP concentration. We show that a molecule's ADP release rate depends exponentially on the applied load, in qualitative agreement with cardiac muscle, which contracts with a velocity inversely proportional to external load. PMID:26239258

Atomic force microscopy studies of human rhinovirus topology and molecular forces.

PubMed

Kienberger, Ferry; Zhu, Rong; Rankl, Christian; Gruber, Hermann J; Blaas, Dieter; Hinterdorfer, Peter

2010-01-01

Dynamic force microscopy (DFM) allows for imaging of the structure and assessment of the function of biological specimens in their physiological environment. In DFM, the cantilever is oscillated at a given frequency and touches the sample only at the end of its downward movement. Accordingly, the problem of lateral forces displacing or even destroying biomolecules is virtually inexistent as the contact time and friction forces are greatly reduced. Here, we describe the use of DFM in studies of human rhinovirus serotype 2 (HRV2). The capsid of HRV2 was reproducibly imaged without any displacement of the virus. Release of the genomic RNA from the virions was initiated by exposure to low-pH buffer and snapshots of the extrusion process were obtained. DFM of the single-stranded RNA genome of an HRV showed loops protruding from a condensed RNA core, 20-50 nm in height. The mechanical rigidity of the RNA was determined by single molecule pulling experiments. From fitting RNA stretching curves to the worm-like-chain (WLC) model a persistence length of 1.0+/-0.17 nm was obtained. Copyright (c) 2010 Elsevier Inc. All rights reserved.

C-5 Propynyl Modifications Enhance the Mechanical Stability of DNA.

PubMed

Aschenbrenner, Daniela; Baumann, Fabian; Milles, Lukas F; Pippig, Diana A; Gaub, Hermann E

2015-07-20

Increased thermal or mechanical stability of DNA duplexes is desired for many applications in nanotechnology or -medicine where DNA is used as a programmable building block. Modifications of pyrimidine bases are known to enhance thermal stability and have the advantage of standard base-pairing and easy integration during chemical DNA synthesis. Through single-molecule force spectroscopy experiments with atomic force microscopy and the molecular force assay we investigated the effect of pyrimidines harboring C-5 propynyl modifications on the mechanical stability of double-stranded DNA. Utilizing these complementary techniques, we show that propynyl bases significantly increase the mechanical stability if the DNA is annealed at high temperature. In contrast, modified DNA complexes formed at room temperature and short incubation times display the same stability as non-modified DNA duplexes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Every Mass or Mass Group When Created Will have No Motion, Linear, Rotational or Vibratory Motion, Singly or in Some Combination, Which May Be Later Modified by External Forces--A Natural Law

NASA Astrophysics Data System (ADS)

Brekke, Stewart

2010-03-01

Every mass or mass group, from atoms and molecules to stars and galaxies,has no motion, is vibrating, rotating,or moving linearly, singularly or in some combination. When created, the excess energy of creation will generate a vibration, rotation and/or linear motion besides the mass or mass group. Curvilinear or orbital motion is linear motion in an external force field. External forces, such as photon, molecular or stellar collisions may over time modify the inital rotational, vibratory or linear motions of the mass of mass group. The energy equation for each mass or mass group is E=mc^2 + 1/2mv^2 + 1/2I2̂+ 1/2kx0^2 + WG+ WE+ WM.

Hydrogen storage capacity on Ti-decorated porous graphene: First-principles investigation

NASA Astrophysics Data System (ADS)

Yuan, Lihua; Kang, Long; Chen, Yuhong; Wang, Daobin; Gong, Jijun; Wang, Chunni; Zhang, Meiling; Wu, Xiaojuan

2018-03-01

Hydrogen storage capacity on Titanium (Ti) decorated porous graphene (PG) has been investigated using density functional theory simulations with generalized gradient approximation method. The possible adsorption sites of Ti atom on PG and electronic properties of Ti-PG system are also discussed.The results show a Ti atom prefers to strongly adsorb on the center site above the C hexagon with the binding energy of 3.65 eV, and the polarization and the hybridization mechanisms both contribute to the Ti atom adsorption on PG. To avoid a tendency of clustering among Ti atoms, the single side of the PG unit cell should only contain one Ti atom. For the single side of PG, four H2 molecules can be adsorbed around Ti atom, and the adsorption mechanism of H2 molecules come from not only the polarization mechanism between Ti and H atoms but also the orbital hybridization among Ti atom, H2 molecules and C atoms. For the case of double sides of PG, eight H2 molecules can be adsorbed on Ti-decorated PG unit cell with the average adsorption energy of -0.457 eV, and the gravimetric hydrogen storage capacity is 6.11 wt.%. Furthermore, ab inito molecular-dynaics simulation result shows that six H2 molecules can be adsorbed on double sides of unit cell of Ti-PG system and the configuration of Ti-PG is very stable at 300 K and without external pressure, which indicates Ti-decorated PG could be considered as a potential hydrogen storage medium at ambient conditions.

On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps.

PubMed

Wang, Jimin

2017-06-01

Partial charges of atoms in a molecule and electrostatic potential (ESP) density for that molecule are known to bear a strong correlation. In order to generate a set of point-field force field parameters for molecular dynamics, Kollman and coworkers have extracted atomic partial charges for each of all 20 amino acids using restrained partial charge-fitting procedures from theoretical ESP density obtained from condensed-state quantum mechanics. The magnitude of atomic partial charges for neutral peptide backbone they have obtained is similar to that of partial atomic charges for ionized carboxylate side chain atoms. In this study, the effect of these known atomic partial charges on ESP is examined using computer simulations and compared with the experimental ESP density recently obtained for proteins using electron microscopy. It is found that the observed ESP density maps are most consistent with the simulations that include atomic partial charges of protein backbone. Therefore, atomic partial charges are integral part of atomic properties in protein molecules and should be included in model refinement. © 2017 The Protein Society.

On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps

PubMed Central

2017-01-01

Abstract Partial charges of atoms in a molecule and electrostatic potential (ESP) density for that molecule are known to bear a strong correlation. In order to generate a set of point‐field force field parameters for molecular dynamics, Kollman and coworkers have extracted atomic partial charges for each of all 20 amino acids using restrained partial charge‐fitting procedures from theoretical ESP density obtained from condensed‐state quantum mechanics. The magnitude of atomic partial charges for neutral peptide backbone they have obtained is similar to that of partial atomic charges for ionized carboxylate side chain atoms. In this study, the effect of these known atomic partial charges on ESP is examined using computer simulations and compared with the experimental ESP density recently obtained for proteins using electron microscopy. It is found that the observed ESP density maps are most consistent with the simulations that include atomic partial charges of protein backbone. Therefore, atomic partial charges are integral part of atomic properties in protein molecules and should be included in model refinement. PMID:28370507

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

PubMed

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.

Engineering giant magnetic anisotropy in single-molecule magnets by dimerizing heavy transition-metal atoms

NASA Astrophysics Data System (ADS)

Qu, Jiaxing; Hu, Jun

2018-05-01

The search for single-molecule magnets with large magnetic anisotropy energy (MAE) is essential for the development of molecular spintronics devices for use at room temperature. Through systematic first-principles calculations, we found that an Os–Os or Ir–Ir dimer embedded in the (5,5‧-Br2-salophen) molecule gives rise to a large MAE of 41.6 or 51.4 meV, respectively, which is large enough to hold the spin orientation at room temperature. Analysis of the electronic structures reveals that the top Os and Ir atoms play the most important part in the total spin moments and large MAEs of the molecules.

Anisotropic charge transport in large single crystals of π-conjugated organic molecules.

PubMed

Hourani, Wael; Rahimi, Khosrow; Botiz, Ioan; Koch, Felix Peter Vinzenz; Reiter, Günter; Lienerth, Peter; Heiser, Thomas; Bubendorff, Jean-Luc; Simon, Laurent

2014-05-07

The electronic properties of organic semiconductors depend strongly on the nature of the molecules, their conjugation and conformation, their mutual distance and the orientation between adjacent molecules. Variations of intramolecular distances and conformation disturb the conjugation and perturb the delocalization of charges. As a result, the mobility considerably decreases compared to that of a covalently well-organized crystal. Here, we present electrical characterization of large single crystals made of the regioregular octamer of 3-hexyl-thiophene (3HT)8 using a conductive-atomic force microscope (C-AFM) in air. We find a large anisotropy in the conduction with charge mobility values depending on the crystallographic orientation of the single crystal. The smaller conduction is in the direction of π-π stacking (along the long axis of the single crystal) with a mobility value in the order of 10(-3) cm(2) V(-1) s(-1), and the larger one is along the molecular axis (in the direction normal to the single crystal surface) with a mobility value in the order of 0.5 cm(2) V(-1) s(-1). The measured current-voltage (I-V) curves showed that along the molecular axis, the current followed an exponential dependence corresponding to an injection mode. In the π-π stacking direction, the current exhibits a space charge limited current (SCLC) behavior, which allows us to estimate the charge carrier mobility.

Single-molecule optomechanics in "picocavities".

PubMed

Benz, Felix; Schmidt, Mikolaj K; Dreismann, Alexander; Chikkaraddy, Rohit; Zhang, Yao; Demetriadou, Angela; Carnegie, Cloudy; Ohadi, Hamid; de Nijs, Bart; Esteban, Ruben; Aizpurua, Javier; Baumberg, Jeremy J

2016-11-11

Trapping light with noble metal nanostructures overcomes the diffraction limit and can confine light to volumes typically on the order of 30 cubic nanometers. We found that individual atomic features inside the gap of a plasmonic nanoassembly can localize light to volumes well below 1 cubic nanometer ("picocavities"), enabling optical experiments on the atomic scale. These atomic features are dynamically formed and disassembled by laser irradiation. Although unstable at room temperature, picocavities can be stabilized at cryogenic temperatures, allowing single atomic cavities to be probed for many minutes. Unlike traditional optomechanical resonators, such extreme optical confinement yields a factor of 10 6 enhancement of optomechanical coupling between the picocavity field and vibrations of individual molecular bonds. This work sets the basis for developing nanoscale nonlinear quantum optics on the single-molecule level. Copyright © 2016, American Association for the Advancement of Science.

The sensing mechanism of N-doped SWCNTs toward SF6 decomposition products: A first-principle study

NASA Astrophysics Data System (ADS)

Gui, Yingang; Tang, Chao; Zhou, Qu; Xu, Lingna; Zhao, Zhongyong; Zhang, Xiaoxing

2018-05-01

In order to monitor the insulation status of SF6-insulated equipment on-line, SOF2 and SO2F2, two typical decomposition products of SF6 under electric discharge condition, are chosen as the target gases to evaluate the type and severity of discharge. In this work, single N atom doping method is adopted to improve the gas sensitivity of single wall carbon nanotubes to SOF2 and SO2F2. Single and double gas molecules adsorptions are considered to completely analyze the adsorption properties of N-doped single wall carbon nanotubes. Calculation results show that N atom doping enhances the surface activity of carbon nanotubes. When gas molecules physically adsorbed on N-doped single wall carbon nanotubes, the weak interaction between gas molecules and N-doped single wall carbon nanotubes nearly not changes the electrical property according to analysis of the density of states and molecular orbitals. While the chemisorption between gas molecules and N-doped single wall carbon nanotubes distinctly decreases the conductivity of adsorption system.

Atomic force microscopy captures length phenotypes in single proteins

PubMed Central

Carrion-Vazquez, Mariano; Marszalek, Piotr E.; Oberhauser, Andres F.; Fernandez, Julio M.

1999-01-01

We use single-protein atomic force microscopy techniques to detect length phenotypes in an Ig module. To gain amino acid resolution, we amplify the mechanical features of a single module by engineering polyproteins composed of up to 12 identical repeats. We show that on mechanical unfolding, mutant polyproteins containing five extra glycine residues added to the folded core of the module extend 20 Å per module farther than the wild-type polyproteins. By contrast, similar insertions near the N or C termini have no effect. Hence, our atomic force microscopy measurements readily discriminate the location of the insert and measure its size with a resolution similar to that of NMR and x-ray crystallography. PMID:10500169

Water's role in the force-induced unfolding of ubiquitin.

PubMed

Li, Jingyuan; Fernandez, Julio M; Berne, B J

2010-11-09

In atomic force spectroscopic studies of the elastomeric protein ubiquitin, the β-strands 1-5 serve as the force clamp. Simulations show how the rupture force in the force-induced unfolding depends on the kinetics of water molecule insertion into positions where they can eventually form hydrogen bonding bridges with the backbone hydrogen bonds in the force-clamp region. The intrusion of water into this region is slowed down by the hydrophobic shielding effect of carbonaceous groups on the surface residues of β-strands 1-5, which thereby regulates water insertion prior to hydrogen bond breakage. The experiments show that the unfolding of the mechanically stressed protein is nonexponential due to static disorder. Our simulations show that different numbers and/or locations of bridging water molecules give rise to a long-lived distribution of transition states and static disorder. We find that slowing down the translational (not rotational) motions of the water molecules by increasing the mass of their oxygen atoms, which leaves the force field and thereby the equilibrium structure of the solvent unchanged, increases the average rupture force; however, the early stages of the force versus time behavior are very similar for our "normal" and fictitious "heavy" water models. Finally, we construct six mutant systems to regulate the hydrophobic shielding effect of the surface residues in the force-clamp region. The mutations in the two termini of β-sheets 1-5 are found to determine a preference for different unfolding pathways and change mutant's average rupture force.

Effect of single-strand break on branch migration and folding dynamics of Holliday junctions.

PubMed

Palets, Dmytro; Lushnikov, Alexander Y; Karymov, Mikhail A; Lyubchenko, Yuri L

2010-09-22

The Holliday junction (HJ), or four-way junction, is a central intermediate state of DNA for homologous genetic recombination and other genetic processes such as replication and repair. Branch migration is the process by which the exchange of homologous DNA regions occurs, and it can be spontaneous or driven by proteins. Unfolding of the HJ is required for branch migration. Our previous single-molecule fluorescence studies led to a model according to which branch migration is a stepwise process consisting of consecutive migration and folding steps. Folding of the HJ in one of the folded conformations terminates the branch migration phase. At the same time, in the unfolded state HJ rapidly migrates over entire homology region of the HJ in one hop. This process can be affected by irregularities in the DNA double helical structure, so mismatches almost terminate a spontaneous branch migration. Single-stranded breaks or nicks are the most ubiquitous defects in the DNA helix; however, to date, their effect on the HJ branch migration has not been studied. In addition, although nicked HJs are specific substrates for a number of enzymes involved in DNA recombination and repair, the role of this substrate specificity remains unclear. Our main goal in this work was to study the effect of nicks on the efficiency of HJ branch migration and the dynamics of the HJ. To accomplish this goal, we applied two single-molecule methods: atomic force microscopy and fluorescence resonance energy transfer. The atomic force microscopy data show that the nick does not prevent branch migration, but it does decrease the probability that the HJ will pass the DNA lesion. The single-molecule fluorescence resonance energy transfer approaches were instrumental in detailing the effects of nicks. These studies reveal a dramatic change of the HJ dynamics. The nick changes the structure and conformational dynamics of the junctions, leading to conformations with geometries that are different from those for the intact HJ. On the basis of these data, we propose a model of branch migration in which the propensity of the junction to unfold decreases the lifetimes of folded states, thereby increasing the frequency of junction fluctuations between the folded states. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Optimized Free Energies from Bidirectional Single-Molecule Force Spectroscopy

NASA Astrophysics Data System (ADS)

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.

Density functional theory study the effects of oxygen-containing functional groups on oxygen molecules and oxygen atoms adsorbed on carbonaceous materials.

PubMed

Qi, Xuejun; Song, Wenwu; Shi, Jianwei

2017-01-01

Density functional theory was used to study the effects of different types of oxygen-containing functional groups on the adsorption of oxygen molecules and single active oxygen atoms on carbonaceous materials. During gasification or combustion reactions of carbonaceous materials, oxygen-containing functional groups such as hydroxyl(-OH), carbonyl(-CO), quinone(-O), and carboxyl(-COOH) are often present on the edge of graphite and can affect graphite's chemical properties. When oxygen-containing functional groups appear on a graphite surface, the oxygen molecules are strongly adsorbed onto the surface to form a four-member ring structure. At the same time, the O-O bond is greatly weakened and easily broken. The adsorption energy value indicates that the adsorption of oxygen molecules changes from physisorption to chemisorption for oxygen-containing functional groups on the edge of a graphite surface. In addition, our results indicate that the adsorption energy depends on the type of oxygen-containing functional group. When a single active oxygen atom is adsorbed on the bridge site of graphite, it gives rise to a stable epoxy structure. Epoxy can cause deformation of the graphite lattice due to the transition of graphite from sp2 to sp3 after the addition of an oxygen atom. For quinone group on the edge of graphite, oxygen atoms react with carbon atoms to form the precursor of CO2. Similarly, the single active oxygen atoms of carbonyl groups can interact with edge carbon atoms to form the precursor of CO2. The results show that oxygen-containing functional groups on graphite surfaces enhance the activity of graphite, which promotes adsorption on the graphite surface.

Density functional theory study the effects of oxygen-containing functional groups on oxygen molecules and oxygen atoms adsorbed on carbonaceous materials

PubMed Central

Song, Wenwu; Shi, Jianwei

2017-01-01

Density functional theory was used to study the effects of different types of oxygen-containing functional groups on the adsorption of oxygen molecules and single active oxygen atoms on carbonaceous materials. During gasification or combustion reactions of carbonaceous materials, oxygen-containing functional groups such as hydroxyl(-OH), carbonyl(-CO), quinone(-O), and carboxyl(-COOH) are often present on the edge of graphite and can affect graphite’s chemical properties. When oxygen-containing functional groups appear on a graphite surface, the oxygen molecules are strongly adsorbed onto the surface to form a four-member ring structure. At the same time, the O-O bond is greatly weakened and easily broken. The adsorption energy value indicates that the adsorption of oxygen molecules changes from physisorption to chemisorption for oxygen-containing functional groups on the edge of a graphite surface. In addition, our results indicate that the adsorption energy depends on the type of oxygen-containing functional group. When a single active oxygen atom is adsorbed on the bridge site of graphite, it gives rise to a stable epoxy structure. Epoxy can cause deformation of the graphite lattice due to the transition of graphite from sp2 to sp3 after the addition of an oxygen atom. For quinone group on the edge of graphite, oxygen atoms react with carbon atoms to form the precursor of CO2. Similarly, the single active oxygen atoms of carbonyl groups can interact with edge carbon atoms to form the precursor of CO2. The results show that oxygen-containing functional groups on graphite surfaces enhance the activity of graphite, which promotes adsorption on the graphite surface. PMID:28301544

Influence of the adsorption geometry of PTCDA on Ag(111) on the tip-molecule forces in non-contact atomic force microscopy.

PubMed

Langewisch, Gernot; Falter, Jens; Schirmeisen, André; Fuchs, Harald

2014-01-01

Perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA) adsorbed on a metal surface is a prototypical organic-anorganic interface. In the past, scanning tunneling microscopy and scanning tunneling spectroscopy studies of PTCDA adsorbed on Ag(111) have revealed differences in the electronic structure of the molecules depending on their adsorption geometry. In the work presented here, high-resolution 3D force spectroscopy measurements at cryogenic temperatures were performed on a surface area that contained a complete PTCDA unit cell with the two possible geometries. At small tip-molecule separations, deviations in the tip-sample forces were found between the two molecule orientations. These deviations can be explained by a different electron density in both cases. This result demonstrates the capability of 3D force spectroscopy to detect even small effects in the electronic properties of organic adsorbates.

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

Sotomayor, Marcos

Hair cell mechanotransduction happens in tens of microseconds, involves forces of a few picoNewtons, and is mediated by nanometer-scale molecular conformational changes. As proteins involved in this process become identified and their high resolution structures become available, multiple tools are being used to explore their “single-molecule responses” to force. Optical tweezers and atomic force microscopy offer exquisite force and extension resolution, but cannot reach the high loading rates expected for high frequency auditory stimuli. Molecular dynamics (MD) simulations can reach these fast time scales, and also provide a unique view of the molecular events underlying protein mechanics, but its predictionsmore » must be experimentally verified. Thus a combination of simulations and experiments might be appropriate to study the molecular mechanics of hearing. Here I review the basics of MD simulations and the different methods used to apply force and study protein mechanics in silico. Simulations of tip link proteins are used to illustrate the advantages and limitations of this method.« less

Electromagnetic tweezers with independent force and torque control

NASA Astrophysics Data System (ADS)

Jiang, Chang; Lionberger, Troy A.; Wiener, Diane M.; Meyhofer, Edgar

2016-08-01

Magnetic tweezers are powerful tools to manipulate and study the mechanical properties of biological molecules and living cells. In this paper we present a novel, bona fide electromagnetic tweezer (EMT) setup that allows independent control of the force and torque applied via micrometer-sized magnetic beads to a molecule under study. We implemented this EMT by combining a single solenoid that generates force (f-EMT) with a set of four solenoids arranged into a symmetric quadrupole to generate torque (τ-EMT). To demonstrate the capability of the tweezers, we attached optically asymmetric Janus beads to single, tethered DNA molecules. We show that tension in the piconewton force range can be applied to single DNA molecules and the molecule can simultaneously be twisted with torques in the piconewton-nanometer range. Furthermore, the EMT allows the two components to be independently controlled. At various force levels applied to the Janus bead, the trap torsional stiffness can be continuously changed simply by varying the current magnitude applied to the τ-EMT. The flexible and independent control of force and torque by the EMT makes it an ideal tool for a range of measurements where tensional and torsional properties need to be studied simultaneously on a molecular or cellular level.

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

PubMed

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.

Peptide adsorption on a hydrophobic surface results from an interplay of solvation, surface, and intrapeptide forces.

PubMed

Horinek, D; Serr, A; Geisler, M; Pirzer, T; Slotta, U; Lud, S Q; Garrido, J A; Scheibel, T; Hugel, T; Netz, R R

2008-02-26

The hydrophobic effect, i.e., the poor solvation of nonpolar parts of molecules, plays a key role in protein folding and more generally for molecular self-assembly and aggregation in aqueous media. The perturbation of the water structure accounts for many aspects of protein hydrophobicity. However, to what extent the dispersion interaction between molecular entities themselves contributes has remained unclear. This is so because in peptide folding interactions and structural changes occur on all length scales and make disentangling various contributions impossible. We address this issue both experimentally and theoretically by looking at the force necessary to peel a mildly hydrophobic single peptide molecule from a flat hydrophobic diamond surface in the presence of water. This setup avoids problems caused by bubble adsorption, cavitation, and slow equilibration that complicate the much-studied geometry with two macroscopic surfaces. Using atomic-force spectroscopy, we determine the mean desorption force of a single spider-silk peptide chain as F = 58 +/- 8 pN, which corresponds to a desorption free energy of approximately 5 k(B)T per amino acid. Our all-atomistic molecular dynamics simulation including explicit water correspondingly yields the desorption force F = 54 +/- 15 pN. This observation demonstrates that standard nonpolarizable force fields used in classical simulations are capable of resolving the fine details of the hydrophobic attraction of peptides. The analysis of the involved energetics shows that water-structure effects and dispersive interactions give contributions of comparable magnitude that largely cancel out. It follows that the correct modeling of peptide hydrophobicity must take the intimate coupling of solvation and dispersive effects into account.

PHYSICAL MODEL FOR RECOGNITION TUNNELING

PubMed Central

Krstić, Predrag; Ashcroft, Brian; Lindsay, Stuart

2015-01-01

Recognition tunneling (RT) identifies target molecules trapped between tunneling electrodes functionalized with recognition molecules that serve as specific chemical linkages between the metal electrodes and the trapped target molecule. Possible applications include single molecule DNA and protein sequencing. This paper addresses several fundamental aspects of RT by multiscale theory, applying both all-atom and coarse-grained DNA models: (1) We show that the magnitude of the observed currents are consistent with the results of non-equilibrium Green's function calculations carried out on a solvated all-atom model. (2) Brownian fluctuations in hydrogen bond-lengths lead to current spikes that are similar to what is observed experimentally. (3) The frequency characteristics of these fluctuations can be used to identify the trapped molecules with a machine-learning algorithm, giving a theoretical underpinning to this new method of identifying single molecule signals. PMID:25650375

Building one molecule from a reservoir of two atoms

NASA Astrophysics Data System (ADS)

Liu, L. R.; Hood, J. D.; Yu, Y.; Zhang, J. T.; Hutzler, N. R.; Rosenband, T.; Ni, K.-K.

2018-05-01

Chemical reactions typically proceed via stochastic encounters between reactants. Going beyond this paradigm, we combined exactly two atoms in a single, controlled reaction. The experimental apparatus traps two individual laser-cooled atoms [one sodium (Na) and one cesium (Cs)] in separate optical tweezers and then merges them into one optical dipole trap. Subsequently, photoassociation forms an excited-state NaCs molecule. The discovery of previously unseen resonances near the molecular dissociation threshold and measurement of collision rates are enabled by the tightly trapped ultracold sample of atoms. As laser-cooling and trapping capabilities are extended to more elements, the technique will enable the study of more diverse, and eventually more complex, molecules in an isolated environment, as well as synthesis of designer molecules for qubits.

Surface based detection schemes for molecular interferometry experiments - implications and possible applications

NASA Astrophysics Data System (ADS)

Juffmann, Thomas; Milic, Adriana; Muellneritsch, Michael; Arndt, Markus

2011-03-01

Surface based detection schemes for molecular interferometry experiments might be crucial in the search for the quantum properties of larger and larger objects since they provide single particle sensitivity. Here we report on molecular interferograms of different biomolecules imaged using fluorescence microscopy. Being able to watch the build-up of an interferogram live and in situ reveals the matter-wave behavior of these complex molecules in an unprecedented way. We examine several problems encountered due to van-der-Waals forces between the molecules and the diffraction grating and discuss possible ways to circumvent these. Especially the advent of ultra-thin (1-100 atomic layers) diffraction masks might path the way towards molecular holography. We also discuss other possible applications such as coherent molecular microscopy.

Low temperature scanning tunneling microscopy of metallic and organic nanostructures

NASA Astrophysics Data System (ADS)

Fölsch, Stefan

2006-03-01

Low temperature scanning tunneling microscopy (LT-STM) is capable of both characterizing and manipulating atomic-scale structures at surfaces. It thus provides a powerful experimental tool to gain fundamental insight into how electronic properties evolve when controlling size, geometry, and composition of nanometric model systems at the level of single atoms and molecules. The experiments discussed in this talk employ a Cu(111) surface onto which perfect nanostructures are assembled from native adatoms and organic molecules. Using single Cu adatoms as building blocks, we obtain zero-, one-, and two-dimensional quantum objects (corresponding to the discrete adatom, monatomic adatom chains, and compact adatom assemblies) with intriguing electronic properties. Depending on the structure shape and the number of incorporated atoms we observe the formation of characteristic quantum levels which merge into the sp-derived Shockley surface state in the limit of extended 2D islands; this state exists on many surfaces, such as Cu(111). Our results reveal the natural linkage between this traditional surface property, the quantum confinement in compact adatom structures, and the quasi-atomic state associated with the single adatom. In a second step, we study the interaction of pentacene (C22H14) with Cu adatom chains serving as model quantum wires. We find that STM-based manipulation is capable of connecting single molecules to the chain ends in a defined way, and that the molecule-chain interaction shifts the chain-localized quantum states to higher binding energies. The present system provides an instructive model case to study single organic molecules interacting with metallic nanostructures. The microscopic nature of such composite structures is of importance for any future molecular-based device realization since it determines the contact conductance between the molecular unit and its metal ''contact pad''.

Fundamental High-Speed Limits in Single-Molecule, Single-Cell, and Nanoscale Force Spectroscopies

PubMed Central

2016-01-01

Force spectroscopy is enhancing our understanding of single-biomolecule, single-cell, and nanoscale mechanics. Force spectroscopy postulates the proportionality between the interaction force and the instantaneous probe deflection. By studying the probe dynamics, we demonstrate that the total force acting on the probe has three different components: the interaction, the hydrodynamic, and the inertial. The amplitudes of those components depend on the ratio between the resonant frequency and the frequency at which the data are measured. A force–distance curve provides a faithful measurement of the interaction force between two molecules when the inertial and hydrodynamic components are negligible. Otherwise, force spectroscopy measurements will underestimate the value of unbinding forces. Neglecting the above force components requires the use of frequency ratios in the 50–500 range. These ratios will limit the use of high-speed methods in force spectroscopy. The theory is supported by numerical simulations. PMID:27359243

Phantom force induced by tunneling current: a characterization on Si(111).

PubMed

Weymouth, A J; Wutscher, T; Welker, J; Hofmann, T; Giessibl, F J

2011-06-03

Simultaneous measurements of tunneling current and atomic forces provide complementary atomic-scale data of the electronic and structural properties of surfaces and adsorbates. With these data, we characterize a strong impact of the tunneling current on the measured force on samples with limited conductivity. The effect is a lowering of the effective gap voltage through sample resistance which in turn lowers the electrostatic attraction, resulting in an apparently repulsive force. This effect is expected to occur on other low-conductance samples, such as adsorbed molecules, and to strongly affect Kelvin probe measurements when tunneling occurs.

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

PubMed

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

2017-08-30

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

Copper Phthalocyanine Functionalized Single-Walled Carbon Nanotubes: Thin Films for Optical Detection.

PubMed

Banimuslem, Hikmat; Hassan, Aseel; Basova, Tamara; Durmuş, Mahmut; Tuncel, Sinem; Esenpinar, Aliye Asli; Gürek, Ayşe Gül; Ahsen, Vefa

2015-03-01

Thin films of non-covalently hybridized single-walled carbon nanotubes (SWCNT) and tetra-substituted copper phthalocyanine (CuPcR4) molecules have been produced from their solutions in dimethylformamide (DMF). FTIR spectra revealed the 7π-7π interaction between SWCNTs and CuPcR4 molecules. DC conductivity of films of acid-treated SWCNT/CuPcR4 hybrid has increased by more than three orders of.magnitude in comparison with conductivity of CuPcR4 films. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) measurements have shown that films obtained from the acid-treated SWCNTs/CuPcR4 hybrids demonstrated more homogenous surface which is ascribed to the highly improved solubility of the hybrid powder in DMF Using total internal reflection ellipsometry spectroscopy (TIRE), thin films of the new hybrid have been examined as an optical sensing membrane for the detection of benzo[a]pyrene in water to demonstrate the sensing properties of the hybrid.

Scanning probe microscopy for the analysis of composite Ti/hydrocarbon plasma polymer thin films

NASA Astrophysics Data System (ADS)

Choukourov, A.; Grinevich, A.; Slavinska, D.; Biederman, H.; Saito, N.; Takai, O.

2008-03-01

Composite Ti/hydrocarbon plasma polymer films with different Ti concentration were deposited on silicon by dc magnetron sputtering of titanium in an atmosphere of argon and hexane. As measured by Kelvin force microscopy and visco-elastic atomic force microscopy, respectively, surface potential and hardness increase with increasing Ti content. Adhesion force to silicon and to fibrinogen molecules was stronger for the Ti-rich films as evaluated from the AFM force-distance curves. Fibrinogen forms a very soft layer on these composites with part of the protein molecules embedded in the outermost region of the plasma polymer. An increase of the surface charge due to fibrinogen adsorption has been observed and attributed to positively charged αC domains of fibrinogen molecule.

Interaction of von Willebrand factor domains with collagen investigated by single molecule force spectroscopy

NASA Astrophysics Data System (ADS)

Posch, Sandra; Obser, Tobias; König, Gesa; Schneppenheim, Reinhard; Tampé, Robert; Hinterdorfer, Peter

2018-03-01

von Willebrand factor (VWF) is a huge multimeric protein that plays a key role in primary hemostasis. Sites for collagen binding, an initial event of hemostasis, are located in the VWF-domains A1 and A3. In this study, we investigated single molecule interactions between collagen surfaces and wild type VWF A1A2A3 domain constructs, as well as clinically relevant VWF A3 domain point mutations, such as p.Ser1731Thr, p.Gln1734His, and p.His1786Arg. For this, we utilized atomic force microscopy based single molecular force spectroscopy. The p.Ser1731Thr mutant had no impact on the VWF-collagen type III and VI interactions, while the p.Gln1734His and p.His1786Arg mutants showed a slight increase in bond stability to collagen type III. This effect probably arises from additional hydrogen bonds that come along with the introduction of these mutations. Using the same mutants, but collagen type VI as a binding partner, resulted in a significant increase in bond stability. VWF domain A1 was reported to be essential for the interaction with collagen type VI and thus our findings strengthen the hypothesis that the VWF A1 domain can compensate for mutations in the VWF A3 domain. Additionally, our data suggest that the mutations could even stabilize the interaction between VWF and collagen without shear. VWF-collagen interactions seem to be an important system in which defective interactions between one VWF domain and one type of collagen can be compensated by alternative binding events.

Soft matter interactions at the molecular scale: interaction forces and energies between single hydrophobic model peptides.

PubMed

Stock, Philipp; Utzig, Thomas; Valtiner, Markus

2017-02-08

In all realms of soft matter research a fundamental understanding of the structure/property relationships based on molecular interactions is crucial for developing a framework for the targeted design of soft materials. However, a molecular picture is often difficult to ascertain and yet essential for understanding the many different competing interactions at play, including entropies and cooperativities, hydration effects, and the enormous design space of soft matter. Here, we characterized for the first time the interaction between single hydrophobic molecules quantitatively using atomic force microscopy, and demonstrated that single molecular hydrophobic interaction free energies are dominated by the area of the smallest interacting hydrophobe. The interaction free energy amounts to 3-4 kT per hydrophobic unit. Also, we find that the transition state of the hydrophobic interactions is located at 3 Å with respect to the ground state, based on Bell-Evans theory. Our results provide a new path for understanding the nature of hydrophobic interactions at the single molecular scale. Our approach enables us to systematically vary hydrophobic and any other interaction type by utilizing peptide chemistry providing a strategic advancement to unravel molecular surface and soft matter interactions at the single molecular scale.

Mathematical analysis of compressive/tensile molecular and nuclear structures

NASA Astrophysics Data System (ADS)

Wang, Dayu

Mathematical analysis in chemistry is a fascinating and critical tool to explain experimental observations. In this dissertation, mathematical methods to present chemical bonding and other structures for many-particle systems are discussed at different levels (molecular, atomic, and nuclear). First, the tetrahedral geometry of single, double, or triple carbon-carbon bonds gives an unsatisfying demonstration of bond lengths, compared to experimental trends. To correct this, Platonic solids and Archimedean solids were evaluated as atoms in covalent carbon or nitrogen bond systems in order to find the best solids for geometric fitting. Pentagonal solids, e.g. the dodecahedron and icosidodecahedron, give the best fit with experimental bond lengths; an ideal pyramidal solid which models covalent bonds was also generated. Second, the macroscopic compression/tension architectural approach was applied to forces at the molecular level, considering atomic interactions as compressive (repulsive) and tensile (attractive) forces. Two particle interactions were considered, followed by a model of the dihydrogen molecule (H2; two protons and two electrons). Dihydrogen was evaluated as two different types of compression/tension structures: a coaxial spring model and a ring model. Using similar methods, covalent diatomic molecules (made up of C, N, O, or F) were evaluated. Finally, the compression/tension model was extended to the nuclear level, based on the observation that nuclei with certain numbers of protons/neutrons (magic numbers) have extra stability compared to other nucleon ratios. A hollow spherical model was developed that combines elements of the classic nuclear shell model and liquid drop model. Nuclear structure and the trend of the "island of stability" for the current and extended periodic table were studied.

Single-molecule dynamic force spectroscopy of the fibronectin-heparin interaction

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

Mitchell, Gabriel; Lamontagne, Charles-Antoine; Lebel, Rejean

2007-12-21

The integrity of cohesive tissues strongly depends on the presence of the extracellular matrix, which provides support and anchorage for cells. The fibronectin protein and the heparin-like glycosaminoglycans are key components of this dynamic structural network. In this report, atomic force spectroscopy was used to gain insight into the compliance and the resistance of the fibronectin-heparin interaction. We found that this interaction can be described by an energetic barrier width of 3.1 {+-} 0.2 A and an off-rate of 0.2 {+-} 0.1 s{sup -1}. These dissociation parameters are similar to those of other carbohydrate-protein interactions and to off-rate values reportedmore » for more complex interactions between cells and extracellular matrix components. Our results indicate that the function of the fibronectin-heparin interaction is supported by its capacity to sustain significant deformations and considerable external mechanical forces.« less

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

PubMed

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

2012-01-10

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

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

PubMed Central

2011-01-01

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

Monitoring single protease activities on triple-helical collagen molecules

NASA Astrophysics Data System (ADS)

Harzar, Raj; Froberg, James; Srivastava, D. K.; Choi, Yongki

Matrix metalloproteinases (MMPs), a particular family of proteases, play a pivotal role in degrading the extracellular matrix (ECM). It has been known for more than 40 years that MMPs are closely involved in multiple human cancers during cell growth, invasion, and metastasis. However, the mechanisms of MMP activity are far from being understood. Here, we monitored enzymatic processing of MMPs with two complementary approaches, atomic force microscopy and nanocircuits measurements. AFM measurements demonstrated that incubation of collagen monomers with MMPs resulted in a single position cleavage, producing 3/4 and 1/4 collagen fragments. From electronic monitoring of single MMP nanocircuit measurements, we were able to capture a single cleavage event with a rate of 0.012 Hz, which were in good agreement with fluorescence assay measurements. This work was supported financially by the NIGMS/NIH (P30GM103332-02) and ND NASA EPSCoR RID Grant.

Prototypical Organic–Oxide Interface: Intramolecular Resolution of Sexiphenyl on In 2O 3 (111)

DOE PAGES

Wagner, Margareta; Hofinger, Jakob; Setvin, Martin; ...

2018-03-28

The performance of an organic semiconductor device is critically determined by the geometric alignment, orientation, and ordering of the organic molecules. Although an organic multilayer eventually adopts the crystal structure of the organic material, the alignment and configuration at the interface with the substrate/electrode material are essential for charge injection into the organic layer. This work focuses on the prototypical organic semiconductor para-sexiphenyl (6P) adsorbed on In 2O 3(111), the thermodynamically most stable surface of the material that the most common transparent conducting oxide, indium tin oxide, is based on. The onset of nucleation and formation of the first monolayermore » are followed with atomically resolved scanning tunneling microscopy and noncontact atomic force microscopy (nc-AFM). Annealing to 200 °C provides sufficient thermal energy for the molecules to orient themselves along the high-symmetry directions of the surface, leading to a single adsorption site. The AFM data suggests an essentially planar adsorption geometry. With increasing coverage, the 6P molecules first form a loose network with a poor long-range order. Eventually, the molecules reorient into an ordered monolayer. In conclusion, this first monolayer has a densely packed, well-ordered (2 × 1) structure with one 6P per In 2O 3(111) substrate unit cell, that is, a molecular density of 5.64 × 10 13 cm –2.« less

Prototypical Organic–Oxide Interface: Intramolecular Resolution of Sexiphenyl on In 2O 3 (111)

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

Wagner, Margareta; Hofinger, Jakob; Setvin, Martin

The performance of an organic semiconductor device is critically determined by the geometric alignment, orientation, and ordering of the organic molecules. Although an organic multilayer eventually adopts the crystal structure of the organic material, the alignment and configuration at the interface with the substrate/electrode material are essential for charge injection into the organic layer. This work focuses on the prototypical organic semiconductor para-sexiphenyl (6P) adsorbed on In 2O 3(111), the thermodynamically most stable surface of the material that the most common transparent conducting oxide, indium tin oxide, is based on. The onset of nucleation and formation of the first monolayermore » are followed with atomically resolved scanning tunneling microscopy and noncontact atomic force microscopy (nc-AFM). Annealing to 200 °C provides sufficient thermal energy for the molecules to orient themselves along the high-symmetry directions of the surface, leading to a single adsorption site. The AFM data suggests an essentially planar adsorption geometry. With increasing coverage, the 6P molecules first form a loose network with a poor long-range order. Eventually, the molecules reorient into an ordered monolayer. In conclusion, this first monolayer has a densely packed, well-ordered (2 × 1) structure with one 6P per In 2O 3(111) substrate unit cell, that is, a molecular density of 5.64 × 10 13 cm –2.« less

Surface structure. Subatomic resolution force microscopy reveals internal structure and adsorption sites of small iron clusters.

PubMed

Emmrich, Matthias; Huber, Ferdinand; Pielmeier, Florian; Welker, Joachim; Hofmann, Thomas; Schneiderbauer, Maximilian; Meuer, Daniel; Polesya, Svitlana; Mankovsky, Sergiy; Ködderitzsch, Diemo; Ebert, Hubert; Giessibl, Franz J

2015-04-17

Clusters built from individual iron atoms adsorbed on surfaces (adatoms) were investigated by atomic force microscopy (AFM) with subatomic resolution. Single copper and iron adatoms appeared as toroidal structures and multiatom clusters as connected structures, showing each individual atom as a torus. For single adatoms, the toroidal shape of the AFM image depends on the bonding symmetry of the adatom to the underlying structure [twofold for copper on copper(110) and threefold for iron on copper(111)]. Density functional theory calculations support the experimental data. The findings correct our previous work, in which multiple minima in the AFM signal were interpreted as a reflection of the orientation of a single front atom, and suggest that dual and triple minima in the force signal are caused by dimer and trimer tips, respectively. Copyright © 2015, American Association for the Advancement of Science.

Capping of Aβ42 Oligomers by Small Molecule Inhibitors

PubMed Central

2015-01-01

Aβ42 peptides associate into soluble oligomers and protofibrils in the process of forming the amyloid fibrils associated with Alzheimer’s disease. The oligomers have been reported to be more toxic to neurons than fibrils, and have been targeted by a wide range of small molecule and peptide inhibitors. With single touch atomic force microscopy (AFM), we show that monomeric Aβ42 forms two distinct types of oligomers, low molecular weight (MW) oligomers with heights of 1–2 nm and high MW oligomers with heights of 3–5 nm. In both cases, the oligomers are disc-shaped with diameters of ∼10–15 nm. The similar diameters suggest that the low MW species stack to form the high MW oligomers. The ability of Aβ42 inhibitors to interact with these oligomers is probed using atomic force microscopy and NMR spectroscopy. We show that curcumin and resveratrol bind to the N-terminus (residues 5–20) of Aβ42 monomers and cap the height of the oligomers that are formed at 1–2 nm. A second class of inhibitors, which includes sulindac sulfide and indomethacin, exhibit very weak interactions across the Aβ42 sequence and do not block the formation of the high MW oligomers. The correlation between N-terminal interactions and capping of the height of the Aβ oligomers provides insights into the mechanism of inhibition and the pathway of Aβ aggregation. PMID:25422864

A programmable DNA origami nanospring that reveals force-induced adjacent binding of myosin VI heads

PubMed Central

Iwaki, M.; Wickham, S. F.; Ikezaki, K.; Yanagida, T.; Shih, W. M.

2016-01-01

Mechanosensitive biological nanomachines such as motor proteins and ion channels regulate diverse cellular behaviour. Combined optical trapping with single-molecule fluorescence imaging provides a powerful methodology to clearly characterize the mechanoresponse, structural dynamics and stability of such nanomachines. However, this system requires complicated experimental geometry, preparation and optics, and is limited by low data-acquisition efficiency. Here we develop a programmable DNA origami nanospring that overcomes these issues. We apply our nanospring to human myosin VI, a mechanosensory motor protein, and demonstrate nanometre-precision single-molecule fluorescence imaging of the individual motor domains (heads) under force. We observe force-induced transitions of myosin VI heads from non-adjacent to adjacent binding, which correspond to adapted roles for low-load and high-load transport, respectively. Our technique extends single-molecule studies under force and clarifies the effect of force on biological processes. PMID:27941751

A programmable DNA origami nanospring that reveals force-induced adjacent binding of myosin VI heads.

PubMed

Iwaki, M; Wickham, S F; Ikezaki, K; Yanagida, T; Shih, W M

2016-12-12

Mechanosensitive biological nanomachines such as motor proteins and ion channels regulate diverse cellular behaviour. Combined optical trapping with single-molecule fluorescence imaging provides a powerful methodology to clearly characterize the mechanoresponse, structural dynamics and stability of such nanomachines. However, this system requires complicated experimental geometry, preparation and optics, and is limited by low data-acquisition efficiency. Here we develop a programmable DNA origami nanospring that overcomes these issues. We apply our nanospring to human myosin VI, a mechanosensory motor protein, and demonstrate nanometre-precision single-molecule fluorescence imaging of the individual motor domains (heads) under force. We observe force-induced transitions of myosin VI heads from non-adjacent to adjacent binding, which correspond to adapted roles for low-load and high-load transport, respectively. Our technique extends single-molecule studies under force and clarifies the effect of force on biological processes.

Single molecule force spectroscopy for in-situ probing oridonin inhibited ROS-mediated EGF-EGFR interactions in living KYSE-150 cells.

PubMed

Pi, Jiang; Jin, Hua; Jiang, Jinhuan; Yang, Fen; Cai, Huaihong; Yang, Peihui; Cai, Jiye; Chen, Zheng W

2017-05-01

As the active anticancer component of Rabdosia Rubescens, oridonin has been proved to show strong anticancer activity in cancer cells, which is also found to be closely related to its specific inhibition effects on the EGFR tyrosine kinase activity. In this study, atomic force microscopy based single molecule force spectroscopy (AFM-SMFS) was used for real-time and in-situ detection of EGF-EGFR interactions in living esophageal cancer KYSE-150 cells to evaluate the anticancer activity of oridonin for the first time. Oridonin was found to induce apoptosis and also reduce EGFR expression in KYSE-150 cells. AFM-SMFS results demonstrated that oridonin could inhibit the binding between EGF and EGFR in KYSE-150 cells by decreasing the unbinding force and binding probability for EGF-EGFR complexes, which was further proved to be closely associated with the intracellular ROS level. More precise mechanism studies based on AFM-SMFS demonstrated that oridonin treatment could decrease the energy barrier width, increase the dissociation off rate constant and decrease the activation energy of EGF-EGFR complexes in ROS dependent way, suggesting oridonin as a strong anticancer agent targeting EGF-EGFR interactions in cancer cells through ROS dependent mechanism. Our results not only suggested oridonin as a strong anticancer agent targeting EGF-EGFR interactions in ROS dependent mechanism, but also highlighted AFM-SMFS as a powerful technique for pharmacodynamic studies by detecting ligand-receptor interactions, which was also expected to be developed into a promising tool for the screening and mechanism studies of drugs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of the molecule-electrode interface on the low-bias conductance of Cu-H2-Cu single-molecule junctions.

PubMed

Jiang, Zhuoling; Wang, Hao; Shen, Ziyong; Sanvito, Stefano; Hou, Shimin

2016-07-28

The atomic structure and electronic transport properties of a single hydrogen molecule connected to both symmetric and asymmetric Cu electrodes are investigated by using the non-equilibrium Green's function formalism combined with the density functional theory. Our calculations show that in symmetric Cu-H2-Cu junctions, the low-bias conductance drops rapidly upon stretching, while asymmetric ones present a low-bias conductance spanning the 0.2-0.3 G0 interval for a wide range of electrode separations. This is in good agreement with experiments on Cu atomic contacts in a hydrogen environment. Furthermore, the distribution of the calculated vibrational energies of the two hydrogen atoms in the asymmetric Cu-H2-Cu junction is also consistent with experiments. These findings provide clear evidence for the formation of asymmetric Cu-H2-Cu molecular junctions in breaking Cu atomic contacts in the presence of hydrogen and are also helpful for the design of molecular devices with Cu electrodes.

Polycyclic aromatic hydrocarbon optical properties and contribution to the acceleration of stellar outflows

NASA Technical Reports Server (NTRS)

Cherchneff, Isabelle; Barker, John R.; Tielens, Alexander G. G. M.

1991-01-01

The optical constants of four polycyclic aromatic hydrocarbon (PAH) molecules (benzene, pyrene, pentacene, and coronene) are determined from their measured laboratory absorption spectra. The Planck mean of the radiation pressure cross section is computed for each molecule and for amorphous carbon (AC) grains, and semiempirically estimated for large PAH molecules up to 400 carbon atoms. Assuming that PAHs are present in carbon-rich stellar outflows, the radiation pressure forces acting on them are calculated and compared with the radiation forces on AC particles. The results show that PAHs possess very different optical properties from AC grains. Small PAHs may experience an 'inverse greenhouse' effect in the inner part of the envelope, as they decouple from the gas close to the photosphere. The radiation pressure force on PAHs is always much less than the force at work on AC grains, and PAH molecules do not affect significantly the dynamics of the outflow.

Entangled photons from single atoms and molecules

NASA Astrophysics Data System (ADS)

Nordén, Bengt

2018-05-01

The first two-photon entanglement experiment performed 50 years ago by Kocher and Commins (KC) provided isolated pairs of entangled photons from an atomic three-state fluorescence cascade. In view of questioning of Bell's theorem, data from these experiments are re-analyzed and shown sufficiently precise to confirm quantum mechanical and dismiss semi-classical theory without need for Bell's inequalities. Polarization photon correlation anisotropy (A) is useful: A is near unity as predicted quantum mechanically and well above the semi-classic range, 0 ⩽ A ⩽ 1 / 2 . Although yet to be found, one may envisage a three-state molecule emitting entangled photon pairs, in analogy with the KC atomic system. Antibunching in fluorescence from single molecules in matrix and entangled photons from quantum dots promise it be possible. Molecules can have advantages to parametric down-conversion as the latter photon distribution is Poissonian and unsuitable for producing isolated pairs of entangled photons. Analytical molecular applications of entangled light are also envisaged.

A measurement of the hysteresis loop in force-spectroscopy curves using a tuning-fork atomic force microscope

PubMed Central

van Vörden, Dennis; Möller, Rolf

2012-01-01

Summary Measurements of the frequency shift versus distance in noncontact atomic force microscopy (NC-AFM) allow measurements of the force gradient between the oscillating tip and a surface (force-spectroscopy measurements). When nonconservative forces act between the tip apex and the surface the oscillation amplitude is damped. The dissipation is caused by bistabilities in the potential energy surface of the tip–sample system, and the process can be understood as a hysteresis of forces between approach and retraction of the tip. In this paper, we present the direct measurement of the whole hysteresis loop in force-spectroscopy curves at 77 K on the PTCDA/Ag/Si(111) √3 × √3 surface by means of a tuning-fork-based NC-AFM with an oscillation amplitude smaller than the distance range of the hysteresis loop. The hysteresis effect is caused by the making and breaking of a bond between PTCDA molecules on the surface and a PTCDA molecule at the tip. The corresponding energy loss was determined to be 0.57 eV by evaluation of the force–distance curves upon approach and retraction. Furthermore, a second dissipation process was identified through the damping of the oscillation while the molecule on the tip is in contact with the surface. This dissipation process occurs mainly during the retraction of the tip. It reaches a maximum value of about 0.22 eV/cycle. PMID:22496993

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

Li, Chunhua; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 45108; Lv, Dashuai

Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regionsmore » between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.« less

Origin of the periodic structure in the conductance curve of gold nanojunctions in hydrogen environment

NASA Astrophysics Data System (ADS)

Jiang, Zhuoling; Wang, Hao; Sanvito, Stefano; Hou, Shimin

2016-03-01

The evolution of the atomic structure and the vibrational and electronic transport properties of gold atomic junctions incorporating molecular and atomic hydrogen upon elongation have been investigated with the nonequilibrium Green's function formalism combined with density functional theory. Our calculations show that for the case of gold junctions doped with a single H2 molecule the low-bias conductance drops rapidly with the electrodes' separation, while it remains almost constant if a single H atom replaces the molecule. In contrast, when one considers two H atoms adsorbed on a gold monatomic chain forming an Au-H-Au-H-Au double-bridge structure, the low-bias conductance increases first and then shows a plateau upon stretching the junction, in perfect agreement with experiments on gold nanocontacts in hydrogen environment. Furthermore, also the distribution of the calculated vibrational energies of the two H atoms is consistent with the experimental result in the low-conductance region, demonstrating clear evidence that hydrogen molecules can dissociate on stretched gold monatomic chains. These findings are helpful to improve our understanding of the structure-property relation of gold nanocontacts and also provide a new prospect for gold nanowires being used as chemical sensors and catalysts.

Mechanochemical Cycloreversion of Cyclobutane Observed at the Single Molecule Level.

PubMed

Pill, Michael F; Holz, Katharina; Preußke, Nils; Berger, Florian; Clausen-Schaumann, Hauke; Lüning, Ulrich; Beyer, Martin K

2016-08-16

Mechanochemical cycloreversion of cyclobutane is known from ultrasound experiments. It is, however, not clear which forces are required to induce the cycloreversion. In atomic force microscopy (AFM) experiments, on the other hand, it is notoriously difficult to assign the ruptured bond. We have solved this problem through the synthesis of tailored macrocycles, in which the cyclobutane mechanophore is bypassed by an ethylene glycol chain of specific length. This macrocycle is covalently anchored between a glass substrate and an AFM cantilever by polyethylene glycol linkers. Upon mechanical stretching of the macrocycle, cycloreversion occurs, which is identified by a defined length increase of the stretched polymer. The measured length change agrees with the value calculated with the external force explicitly included (EFEI) method. By using two different lengths for the ethylene glycol safety line, the assignment becomes unambiguous. Mechanochemical cycloreversion of cyclobutane is observed at forces above 1.7 nN. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Single molecules and single nanoparticles as windows to the nanoscale

NASA Astrophysics Data System (ADS)

Caldarola, Martín; Orrit, Michel

2018-05-01

Since the first optical detection of single molecules, they have been used as nanometersized optical sensors to explore the physical properties of materials and light-matter interaction at the nanoscale. Understanding nanoscale properties of materials is fundamental for the development of new technology that requires precise control of atoms and molecules when the quantum nature of matter cannot be ignored. In the following lines, we illustrate this journey into nanoscience with some experiments from our group.

Force Induced Globule-to-Coil Transition of Single Polymer Chains.

NASA Astrophysics Data System (ADS)

Gunari, Nikhil; Walker, Gilbert

2008-03-01

Force induced structural transitions of individual homopolymer chains have been studied in different solvent conditions using single molecule force spectroscopy. Single molecule mechanics in the ``fly-fishing'' mode showed a first-order like transition for polystyrene (PS) in water exhibiting a characteristic three regime force extension curve. In contrast, poly methylmethacrylate (PMMA) showed a characteristic saw-tooth pattern reminiscent of multidomain disassembly behavior similar to that seen in modular protein mechanics. The plateau force for PS and the saw-tooth pattern for PMMA disappear when measured in aqueous guanidine hydrochloride solution and in other non-solvents showing that the characteristic deformational behavior observed for the two polymers in water may be due to hydrophobic interactions .

Conservative and dissipative force imaging of switchable rotaxanes with frequency-modulation atomic force microscopy

NASA Astrophysics Data System (ADS)

Farrell, Alan A.; Fukuma, Takeshi; Uchihashi, Takayuki; Kay, Euan R.; Bottari, Giovanni; Leigh, David A.; Yamada, Hirofumi; Jarvis, Suzanne P.

2005-09-01

We compare constant amplitude frequency modulation atomic force microscopy (FM-AFM) in ambient conditions to ultrahigh vacuum (UHV) experiments by analysis of thin films of rotaxane molecules. Working in ambient conditions is important for the development of real-world molecular devices. We show that the FM-AFM technique allows quantitative measurement of conservative and dissipative forces without instabilities caused by any native water layer. Molecular resolution is achieved despite the low Q-factor in the air. Furthermore, contrast in the energy dissipation is observed even at the molecular level. This should allow investigations into stimuli-induced sub-molecular motion of organic films.

R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries

PubMed Central

Dupradeau, François-Yves; Cézard, Christine; Lelong, Rodolphe; Stanislawiak, Élodie; Pêcher, Julien; Delepine, Jean Charles; Cieplak, Piotr

2008-01-01

The web-based RESP ESP charge DataBase (R.E.DD.B., http://q4md-forcefieldtools.org/REDDB) is a free and new source of RESP and ESP atomic charge values and force field libraries for model systems and/or small molecules. R.E.DD.B. stores highly effective and reproducible charge values and molecular structures in the Tripos mol2 file format, information about the charge derivation procedure, scripts to integrate the charges and molecular topology in the most common molecular dynamics packages. Moreover, R.E.DD.B. allows users to freely store and distribute RESP or ESP charges and force field libraries to the scientific community, via a web interface. The first version of R.E.DD.B., released in January 2006, contains force field libraries for molecules as well as molecular fragments for standard residues and their analogs (amino acids, monosaccharides, nucleotides and ligands), hence covering a vast area of relevant biological applications. PMID:17962302

Behavior of P85 and P188 Poloxamer Molecules: Computer Simulations Using United Atom Force Field.

DOE PAGES

Goliaei, Ardeshir; Lau, Edmond Y.; Adhikari, Upendra; ...

2016-05-27

To study the interaction between poloxamer molecules and lipid bilayers using molecular dynamics simulation technique with the united atom resolution, we augmented the GROMOS force field to include poloxamers. We validated the force field by calculating the radii of gyration of two poloxamers, P85 and P188, solvated in water and by considering the poloxamer density distributions at the air/water interface. The emphasis of our simulations was on the study of the interaction between poloxamers and lipid bilayer. At the water/lipid bilayer interface, we observed that both poloxamers studied, P85 and P188, behaved like surfactants: the hydrophilic blocks of poloxamers becamemore » adsorbed at the polar interface, while their hydrophobic block penetrated the interface into the aliphatic tail region of the lipid bilayer. We also observed that when P85 and P188 poloxamers interacted with damaged membranes that contained pores, the hydrophobic blocks of copolymers penetrated into the membrane in the vicinity of the pore and compressed the membrane. Lastly, due to this compression, water molecules were evacuated from the pore.« less

Quantitative assessment of intermolecular interactions by atomic force microscopy imaging using copper oxide tips

NASA Astrophysics Data System (ADS)

Mönig, Harry; Amirjalayer, Saeed; Timmer, Alexander; Hu, Zhixin; Liu, Lacheng; Díaz Arado, Oscar; Cnudde, Marvin; Strassert, Cristian Alejandro; Ji, Wei; Rohlfing, Michael; Fuchs, Harald

2018-05-01

Atomic force microscopy is an impressive tool with which to directly resolve the bonding structure of organic compounds1-5. The methodology usually involves chemical passivation of the probe-tip termination by attaching single molecules or atoms such as CO or Xe (refs 1,6-9). However, these probe particles are only weakly connected to the metallic apex, which results in considerable dynamic deflection. This probe particle deflection leads to pronounced image distortions, systematic overestimation of bond lengths, and in some cases even spurious bond-like contrast features, thus inhibiting reliable data interpretation8-12. Recently, an alternative approach to tip passivation has been used in which slightly indenting a tip into oxidized copper substrates and subsequent contrast analysis allows for the verification of an oxygen-terminated Cu tip13-15. Here we show that, due to the covalently bound configuration of the terminal oxygen atom, this copper oxide tip (CuOx tip) has a high structural stability, allowing not only a quantitative determination of individual bond lengths and access to bond order effects, but also reliable intermolecular bond characterization. In particular, by removing the previous limitations of flexible probe particles, we are able to provide conclusive experimental evidence for an unusual intermolecular N-Au-N three-centre bond. Furthermore, we demonstrate that CuOx tips allow the characterization of the strength and configuration of individual hydrogen bonds within a molecular assembly.

Extracting physics of life at the molecular level: A review of single-molecule data analyses.

PubMed

Colomb, Warren; Sarkar, Susanta K

2015-06-01

Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques. Copyright © 2015 Elsevier B.V. All rights reserved.

Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra

NASA Astrophysics Data System (ADS)

Cukras, Janusz; Coriani, Sonia; Decleva, Piero; Christiansen, Ove; Norman, Patrick

2013-09-01

A recently implemented asymmetric Lanczos algorithm for computing (complex) linear response functions within the coupled cluster singles (CCS), coupled cluster singles and iterative approximate doubles (CC2), and coupled cluster singles and doubles (CCSD) is coupled to a Stieltjes imaging technique in order to describe the photoionization cross section of atoms and molecules, in the spirit of a similar procedure recently proposed by Averbukh and co-workers within the Algebraic Diagrammatic Construction approach. Pilot results are reported for the atoms He, Ne, and Ar and for the molecules H2, H2O, NH3, HF, CO, and CO2.

Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra.

PubMed

Cukras, Janusz; Coriani, Sonia; Decleva, Piero; Christiansen, Ove; Norman, Patrick

2013-09-07

A recently implemented asymmetric Lanczos algorithm for computing (complex) linear response functions within the coupled cluster singles (CCS), coupled cluster singles and iterative approximate doubles (CC2), and coupled cluster singles and doubles (CCSD) is coupled to a Stieltjes imaging technique in order to describe the photoionization cross section of atoms and molecules, in the spirit of a similar procedure recently proposed by Averbukh and co-workers within the Algebraic Diagrammatic Construction approach. Pilot results are reported for the atoms He, Ne, and Ar and for the molecules H2, H2O, NH3, HF, CO, and CO2.

Mapping power-law rheology of living cells using multi-frequency force modulation atomic force microscopy

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

Takahashi, Ryosuke; Okajima, Takaharu, E-mail: okajima@ist.hokudai.ac.jp

We present multi-frequency force modulation atomic force microscopy (AFM) for mapping the complex shear modulus G* of living cells as a function of frequency over the range of 50–500 Hz in the same measurement time as the single-frequency force modulation measurement. The AFM technique enables us to reconstruct image maps of rheological parameters, which exhibit a frequency-dependent power-law behavior with respect to G{sup *}. These quantitative rheological measurements reveal a large spatial variation in G* in this frequency range for single cells. Moreover, we find that the reconstructed images of the power-law rheological parameters are much different from those obtained inmore » force-curve or single-frequency force modulation measurements. This indicates that the former provide information about intracellular mechanical structures of the cells that are usually not resolved with the conventional force measurement methods.« less

Effect of molecular asymmetry on the charge transport physics of high mobility n-type molecular semiconductors investigated by scanning Kelvin probe microscopy.

PubMed

Hu, Yuanyuan; Berdunov, Nikolai; Di, Chong-an; Nandhakumar, Iris; Zhang, Fengjiao; Gao, Xike; Zhu, Daoben; Sirringhaus, Henning

2014-07-22

We have investigated the influence of the symmetry of the side chain substituents in high-mobility, solution processable n-type molecular semiconductors on the performance of organic field-effect transistors (OFETs). We compare two molecules with the same conjugated core, but either symmetric or asymmetric side chain substituents, and investigate the transport properties and thin film growth mode using scanning Kelvin probe microscopy (SKPM) and atomic force microscopy (AFM). We find that asymmetric side chains can induce a favorable two-dimensional growth mode with a bilayer structure, which enables ultrathin films with a single bilayer to exhibit excellent transport properties, while the symmetric molecules adopt an unfavorable three-dimensional growth mode in which transport in the first monolayer at the interface is severely hindered by high-resistance grain boundaries.

Electromagnetic torque tweezers: a versatile approach for measurement of single-molecule twist and torque.

PubMed

Janssen, Xander J A; Lipfert, Jan; Jager, Tessa; Daudey, Renier; Beekman, Jaap; Dekker, Nynke H

2012-07-11

The well-established single-molecule force-spectroscopy techniques have recently been complemented by methods that can measure torque and twist directly, notably magnetic torque tweezers and the optical torque wrench. A limitation of the current torque measurement schemes is the intrinsic coupling between the force and torque degrees of freedom. Here we present electromagnetic torque tweezers (eMTT) that combine permanent and electromagnets to enable independent control of the force and torsional trap stiffness for sensitive measurements of single molecule torque and twist. Using the eMTT, we demonstrate sensitive torque measurements on tethered DNA molecules from simple tracking of the beads' (x,y)-position, obviating the need for any angular tracking algorithms or markers. Employing the eMTT for high-resolution torque measurements, we experimentally confirm the theoretically predicted torque overshoot at the DNA buckling transition in high salt conditions. We envision that the flexibility and control afforded by the eMTT will enable a range of new torque and twist measurement schemes from single-molecules to living cells.

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

PubMed

Polok, Kamil

2018-02-08

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

Motor-motor interactions in ensembles of muscle myosin: using theory to connect single molecule to ensemble measurements

NASA Astrophysics Data System (ADS)

Walcott, Sam

2013-03-01

Interactions between the proteins actin and myosin drive muscle contraction. Properties of a single myosin interacting with an actin filament are largely known, but a trillion myosins work together in muscle. We are interested in how single-molecule properties relate to ensemble function. Myosin's reaction rates depend on force, so ensemble models keep track of both molecular state and force on each molecule. These models make subtle predictions, e.g. that myosin, when part of an ensemble, moves actin faster than when isolated. This acceleration arises because forces between molecules speed reaction kinetics. Experiments support this prediction and allow parameter estimates. A model based on this analysis describes experiments from single molecule to ensemble. In vivo, actin is regulated by proteins that, when present, cause the binding of one myosin to speed the binding of its neighbors; binding becomes cooperative. Although such interactions preclude the mean field approximation, a set of linear ODEs describes these ensembles under simplified experimental conditions. In these experiments cooperativity is strong, with the binding of one molecule affecting ten neighbors on either side. We progress toward a description of myosin ensembles under physiological conditions.

Fast flexible modeling of RNA structure using internal coordinates.

PubMed

Flores, Samuel Coulbourn; Sherman, Michael A; Bruns, Christopher M; Eastman, Peter; Altman, Russ Biagio

2011-01-01

Modeling the structure and dynamics of large macromolecules remains a critical challenge. Molecular dynamics (MD) simulations are expensive because they model every atom independently, and are difficult to combine with experimentally derived knowledge. Assembly of molecules using fragments from libraries relies on the database of known structures and thus may not work for novel motifs. Coarse-grained modeling methods have yielded good results on large molecules but can suffer from difficulties in creating more detailed full atomic realizations. There is therefore a need for molecular modeling algorithms that remain chemically accurate and economical for large molecules, do not rely on fragment libraries, and can incorporate experimental information. RNABuilder works in the internal coordinate space of dihedral angles and thus has time requirements proportional to the number of moving parts rather than the number of atoms. It provides accurate physics-based response to applied forces, but also allows user-specified forces for incorporating experimental information. A particular strength of RNABuilder is that all Leontis-Westhof basepairs can be specified as primitives by the user to be satisfied during model construction. We apply RNABuilder to predict the structure of an RNA molecule with 160 bases from its secondary structure, as well as experimental information. Our model matches the known structure to 10.2 Angstroms RMSD and has low computational expense.

From Artificial Atoms to Nanocrystal Molecules: Preparation and Properties of More Complex Nanostructures

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

Choi, Charina L; Alivisatos, A Paul

2009-10-20

Quantum dots, which have found widespread use in fields such as biomedicine, photovoltaics, and electronics, are often called artificial atoms due to their size-dependent physical properties. Here this analogy is extended to consider artificial nanocrystal molecules, formed from well-defined groupings of plasmonically or electronically coupled single nanocrystals. Just as a hydrogen molecule has properties distinct from two uncoupled hydrogen atoms, a key feature of nanocrystal molecules is that they exhibit properties altered from those of the component nanoparticles due to coupling. The nature of the coupling between nanocrystal atoms and its response to vibrations and deformations of the nanocrystal moleculemore » bonds are of particular interest. We discuss synthetic approaches, predicted and observed physical properties, and prospects and challenges toward this new class of materials.« less

Potential energy surfaces of the low-lying electronic states of the Li + LiCs system

NASA Astrophysics Data System (ADS)

Jasik, P.; Kilich, T.; Kozicki, J.; Sienkiewicz, J. E.

2018-03-01

Ab initio quantum chemistry calculations are performed for the mixed alkali triatomic system. Global minima of the ground and first excited doublet states of the trimer are found and Born-Oppenheimer potential energy surfaces of the Li atom interacting with the LiCs molecule were calculated for these states. The lithium atom is placed at various distances and bond angles from the lithium-caesium dimer. Three-body nonadditive forces of the Li2Cs molecule in the global minimum are investigated. Dimer-atom interactions are found to be strongly attractive and may be important in the experiments, particularly involving cold alkali polar dimers.

Chemical control of electrical contact to sp² carbon atoms.

PubMed

Frederiksen, Thomas; Foti, Giuseppe; Scheurer, Fabrice; Speisser, Virginie; Schull, Guillaume

2014-04-16

Carbon-based nanostructures are attracting tremendous interest as components in ultrafast electronics and optoelectronics. The electrical interfaces to these structures play a crucial role for the electron transport, but the lack of control at the atomic scale can hamper device functionality and integration into operating circuitry. Here we study a prototype carbon-based molecular junction consisting of a single C60 molecule and probe how the electric current through the junction depends on the chemical nature of the foremost electrode atom in contact with the molecule. We find that the efficiency of charge injection to a C60 molecule varies substantially for the considered metallic species, and demonstrate that the relative strength of the metal-C bond can be extracted from our transport measurements. Our study further suggests that a single-C60 junction is a basic model to explore the properties of electrical contacts to meso- and macroscopic sp(2) carbon structures.

Chemical control of electrical contact to sp2 carbon atoms

NASA Astrophysics Data System (ADS)

Frederiksen, Thomas; Foti, Giuseppe; Scheurer, Fabrice; Speisser, Virginie; Schull, Guillaume

2014-04-01

Carbon-based nanostructures are attracting tremendous interest as components in ultrafast electronics and optoelectronics. The electrical interfaces to these structures play a crucial role for the electron transport, but the lack of control at the atomic scale can hamper device functionality and integration into operating circuitry. Here we study a prototype carbon-based molecular junction consisting of a single C60 molecule and probe how the electric current through the junction depends on the chemical nature of the foremost electrode atom in contact with the molecule. We find that the efficiency of charge injection to a C60 molecule varies substantially for the considered metallic species, and demonstrate that the relative strength of the metal-C bond can be extracted from our transport measurements. Our study further suggests that a single-C60 junction is a basic model to explore the properties of electrical contacts to meso- and macroscopic sp2 carbon structures.

Frequency modulation atomic force microscopy: a dynamic measurement technique for biological systems

NASA Astrophysics Data System (ADS)

Higgins, Michael J.; Riener, Christian K.; Uchihashi, Takayuki; Sader, John E.; McKendry, Rachel; Jarvis, Suzanne P.

2005-03-01

Frequency modulation atomic force microscopy (FM-AFM) has been modified to operate in a liquid environment within an atomic force microscope specifically designed for investigating biological samples. We demonstrate the applicability of FM-AFM to biological samples using the spectroscopy mode to measure the unbinding forces of a single receptor-ligand (biotin-avidin) interaction. We show that quantitative adhesion force measurements can only be obtained provided certain modifications are made to the existing theory, which is used to convert the detected frequency shifts to an interaction force. Quantitative force measurements revealed that the unbinding forces for the biotin-avidin interaction were greater than those reported in previous studies. This finding was due to the use of high average tip velocities, which were calculated to be two orders of magnitude greater than those typically used in unbinding receptor-ligand experiments. This study therefore highlights the potential use of FM-AFM to study a range of biological systems, including living cells and/or single biomolecule interactions.

Single-Atom Catalyst of Platinum Supported on Titanium Nitride for Selective Electrochemical Reactions.

PubMed

Yang, Sungeun; Kim, Jiwhan; Tak, Young Joo; Soon, Aloysius; Lee, Hyunjoo

2016-02-05

As a catalyst, single-atom platinum may provide an ideal structure for platinum minimization. Herein, a single-atom catalyst of platinum supported on titanium nitride nanoparticles were successfully prepared with the aid of chlorine ligands. Unlike platinum nanoparticles, the single-atom active sites predominantly produced hydrogen peroxide in the electrochemical oxygen reduction with the highest mass activity reported so far. The electrocatalytic oxidation of small organic molecules, such as formic acid and methanol, also exhibited unique selectivity on the single-atom platinum catalyst. A lack of platinum ensemble sites changed the reaction pathway for the oxygen-reduction reaction toward a two-electron pathway and formic acid oxidation toward direct dehydrogenation, and also induced no activity for the methanol oxidation. This work demonstrates that single-atom platinum can be an efficient electrocatalyst with high mass activity and unique selectivity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lorentz-like force emerging from kinematic interactions between electrons and nuclei in molecules: A quantum mechanical origin of symmetry breaking that can trigger molecular chirality.

PubMed

Takatsuka, Kazuo

2017-02-28

The Longuet-Higgins (Berry) phase arising from nonadiabatic dynamics and the Aharonov-Bohm phase associated with the dynamics of a charged particle in the electromagnetic vector potential are well known to be individually a manifestation of a class of the so-called geometrical phase. We herein discuss another similarity between the force working on a charged particle moving in a magnetic field, the Lorentz force, and a force working on nuclei while passing across a region where they have a strong quantum mechanical kinematic (nonadiabatic) coupling with electrons in a molecule. This kinematic force is indeed akin to the Lorentz force in that its magnitude is proportional to the velocity of the relevant nuclei and works in the direction perpendicular to its translational motion. Therefore this Lorentz-like nonadiabatic force is realized only in space of more or equal to three dimensions, thereby highlighting a truly multi-dimensional effect of nonadiabatic interaction. We investigate its physical significance qualitatively in the context of breaking of molecular spatial symmetry, which is not seen otherwise without this force. This particular symmetry breaking is demonstrated in application to a coplanar collision between a planar molecule and an atom sharing the same plane. We show that the atom is guided by this force to the direction out from the plane, resulting in a configuration that distinguishes one side of the mirror plane from the other. This can serve as a trigger for the dynamics towards molecular chirality.

Probing physical properties at the nanoscale using atomic force microscopy

NASA Astrophysics Data System (ADS)

Ditzler, Lindsay Rachel

Techniques that measure physical properties at the nanoscale with high sensitivity are significantly limited considering the number of new nanomaterials being developed. The development of atomic force microscopy (AFM) has lead to significant advancements in the ability to characterize physical properties of materials in all areas of science: chemistry, physics, engineering, and biology have made great scientific strides do to the versatility of the AFM. AFM is used for quantification of many physical properties such as morphology, electrical, mechanical, magnetic, electrochemical, binding interactions, and protein folding. This work examines the electrical and mechanical properties of materials applicable to the field of nano-electronics. As electronic devices are miniaturized the demand for materials with unique electrical properties, which can be developed and exploited, has increased. For example, discussed in this work, a derivative of tetrathiafulvalene, which exhibits a unique loss of conductivity upon compression of the self-assembled monolayer could be developed into a molecular switch. This work also compares tunable organic (tetraphenylethylene tetracarboxylic acid and bis(pyridine)s assemblies) and metal-organic (Silver-stilbizole coordination compounds) crystals which show high electrical conductivity. The electrical properties of these materials vary depending on their composition allowing for the development of compositionally tunable functional materials. Additional work was done to investigate the effects of molecular environment on redox active 11-ferroceneyl-1 undecanethiol (Fc) molecules. The redox process of mixed monolayers of Fc and decanethiol was measured using conductive probe atomic force microscopy and force spectroscopy. As the concentration of Fc increased large, variations in the force were observed. Using these variations the number of oxidized molecules in the monolayer was determined. AFM is additionally capable of investigating interactions at the nanoscale, such as ligand-receptor interactions. This work examines the interactions between the enzyme dihydrofolate reductase (DHFR), a widely investigated enzyme targeted for cancer and antimicrobial pharmaceutical, and methotrexate (MTX), a strong competitive inhibitor of DHFR. The DHFR was immobilized on a gold substrate, bound through a single surface cysteine, and maintained catalytic activity. AFM probe was functionalized with MTX and the interaction strength was measured using AFM. This work highlights the versatility of AFM, specifically force spectroscopy for the quantification of electrical, mechanical, and ligand-receptor interactions at the nanoscale.

Prediction of Water Binding to Protein Hydration Sites with a Discrete, Semiexplicit Solvent Model.

PubMed

Setny, Piotr

2015-12-08

Buried water molecules are ubiquitous in protein structures and are found at the interface of most protein-ligand complexes. Determining their distribution and thermodynamic effect is a challenging yet important task, of great of practical value for the modeling of biomolecular structures and their interactions. In this study, we present a novel method aimed at the prediction of buried water molecules in protein structures and estimation of their binding free energies. It is based on a semiexplicit, discrete solvation model, which we previously introduced in the context of small molecule hydration. The method is applicable to all macromolecular structures described by a standard all-atom force field, and predicts complete solvent distribution within a single run with modest computational cost. We demonstrate that it indicates positions of buried hydration sites, including those filled by more than one water molecule, and accurately differentiates them from sterically accessible to water but void regions. The obtained estimates of water binding free energies are in fair agreement with reference results determined with the double decoupling method.

Structured Water Layers Adjacent to Biological Membranes

PubMed Central

Higgins, Michael J.; Polcik, Martin; Fukuma, Takeshi; Sader, John E.; Nakayama, Yoshikazu; Jarvis, Suzanne P.

2006-01-01

Water amid the restricted space of crowded biological macromolecules and at membrane interfaces is essential for cell function, though the structure and function of this “biological water” itself remains poorly defined. The force required to remove strongly bound water is referred to as the hydration force and due to its widespread importance, it has been studied in numerous systems. Here, by using a highly sensitive dynamic atomic force microscope technique in conjunction with a carbon nanotube probe, we reveal a hydration force with an oscillatory profile that reflects the removal of up to five structured water layers from between the probe and biological membrane surface. Further, we find that the hydration force can be modified by changing the membrane fluidity. For 1,2-dipalmitoyl-sn-glycero-3-phosphocholine gel (Lβ) phase bilayers, each oscillation in the force profile indicates the force required to displace a single layer of water molecules from between the probe and bilayer. In contrast, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine fluid (Lα) phase bilayers at 60°C and 1,2-dioleoyl-sn-glycero-3-phosphocholine fluid (Lα) phase bilayers at 24°C seriously disrupt the molecular ordering of the water and result predominantly in a monotonic force profile. PMID:16798815

Symmetry of Carrier-Envelope Phase Difference Effects in Strong-Field, Few-Cycle Ionization of Atoms and Molecules

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

Martiny, Christian Per Juul; Madsen, Lars Bojer

2006-09-01

In few-cycle pulses, the exact value of the carrier-envelope phase difference (CEPD) has a pronounced influence on the ionization dynamics of atoms and molecules. We show that, for atoms in circularly polarized light, a change in the CEPD is mapped uniquely to an overall rotation of the system, and results for arbitrary CEPD are obtained by rotation of the results from a single calculation with fixed CEPD. For molecules, this is true only for linear molecules aligned parallel with the propagation direction of the field. The effects of CEPD are classified as geometric or nongeometric. The observations are exemplified bymore » strong-field calculations on hydrogen.« less

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

PubMed

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.

Adsorption orientations and immunological recognition of antibodies on graphene

NASA Astrophysics Data System (ADS)

Vilhena, J. G.; Dumitru, A. C.; Herruzo, Elena T.; Mendieta-Moreno, Jesús I.; Garcia, Ricardo; Serena, P. A.; Pérez, Rubén

2016-07-01

Large-scale molecular dynamics (MD) simulations and atomic force microscopy (AFM) in liquid are combined to characterize the adsorption of Immunoglobulin G (IgG) antibodies over a hydrophobic surface modeled with a three-layer graphene slab. We consider explicitly the water solvent, simulating systems with massive sizes (up to 770 000 atoms), for four different adsorption orientations. Protocols based on steered MD to speed up the protein diffusion stage and to enhance the dehydration process are combined with long simulation times (>150 ns) in order to make sure that the final adsorption states correspond to actual stable configurations. Our MD results and the AFM images demonstrate that the IgG antibodies are strongly adsorbed, do not unfold, and retain their secondary and tertiary structures upon deposition. Statistical analysis of the AFM images shows that many of the antibodies adopt vertical orientations, even at very small coverages, which expose at least one Fab binding site for recognition events. Single molecule force spectroscopy experiments demonstrate the immunological response of the deposited antibodies by recognizing its specific antigens. The above properties together with the strong anchoring and preservation of the secondary structure, make graphene an excellent candidate for the development of immunosensors.Large-scale molecular dynamics (MD) simulations and atomic force microscopy (AFM) in liquid are combined to characterize the adsorption of Immunoglobulin G (IgG) antibodies over a hydrophobic surface modeled with a three-layer graphene slab. We consider explicitly the water solvent, simulating systems with massive sizes (up to 770 000 atoms), for four different adsorption orientations. Protocols based on steered MD to speed up the protein diffusion stage and to enhance the dehydration process are combined with long simulation times (>150 ns) in order to make sure that the final adsorption states correspond to actual stable configurations. Our MD results and the AFM images demonstrate that the IgG antibodies are strongly adsorbed, do not unfold, and retain their secondary and tertiary structures upon deposition. Statistical analysis of the AFM images shows that many of the antibodies adopt vertical orientations, even at very small coverages, which expose at least one Fab binding site for recognition events. Single molecule force spectroscopy experiments demonstrate the immunological response of the deposited antibodies by recognizing its specific antigens. The above properties together with the strong anchoring and preservation of the secondary structure, make graphene an excellent candidate for the development of immunosensors. Electronic supplementary information (ESI) available: Further details concerning the experimental methods, the MD simulation protocols, and the characterization and stability of the different adsorption configurations. See DOI: 10.1039/C5NR07612A

Single molecule force measurements of perlecan/HSPG2: A key component of the osteocyte pericellular matrix.

PubMed

Wijeratne, Sithara S; Martinez, Jerahme R; Grindel, Brian J; Frey, Eric W; Li, Jingqiang; Wang, Liyun; Farach-Carson, Mary C; Kiang, Ching-Hwa

2016-03-01

Perlecan/HSPG2, a large, monomeric heparan sulfate proteoglycan (HSPG), is a key component of the lacunar canalicular system (LCS) of cortical bone, where it is part of the mechanosensing pericellular matrix (PCM) surrounding the osteocytic processes and serves as a tethering element that connects the osteocyte cell body to the bone matrix. Within the pericellular space surrounding the osteocyte cell body, perlecan can experience physiological fluid flow drag force and in that capacity function as a sensor to relay external stimuli to the osteocyte cell membrane. We previously showed that a reduction in perlecan secretion alters the PCM fiber composition and interferes with bone's response to a mechanical loading in vivo. To test our hypothesis that perlecan core protein can sustain tensile forces without unfolding under physiological loading conditions, atomic force microscopy (AFM) was used to capture images of perlecan monomers at nanoscale resolution and to perform single molecule force measurement (SMFMs). We found that the core protein of purified full-length human perlecan is of suitable size to span the pericellular space of the LCS, with a measured end-to-end length of 170±20 nm and a diameter of 2-4 nm. Force pulling revealed a strong protein core that can withstand over 100 pN of tension well over the drag forces that are estimated to be exerted on the individual osteocyte tethers. Data fitting with an extensible worm-like chain model showed that the perlecan protein core has a mean elastic constant of 890 pN and a corresponding Young's modulus of 71 MPa. We conclude that perlecan has physical properties that would allow it to act as a strong but elastic tether in the LCS. Copyright © 2015 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.

Nanomechanical and thermophoretic analyses of the nucleotide-dependent interactions between the AAA + subunits of magnesium chelatase

DOE PAGES

Adams, Nathan B. P.; Vasilev, Cvetelin; Brindley, Amanda A.; ...

2016-04-30

In chlorophyll biosynthesis, the magnesium chelatase enzyme complex catalyzes the insertion of a Mg 2+ ion into protoporphyrin IX. Prior to this event, two of the three subunits, the AAA + proteins ChlI and ChlD, form a ChlID–MgATP complex. We used microscale thermophoresis to directly determine dissociation constants for the I-D subunits from Synechocystis, and to show that the formation of a ChlID–MgADP complex, mediated by the arginine finger and the sensor II domain on ChlD, is necessary for the assembly of the catalytically active ChlHID–MgATP complex. The N-terminal AAA + domain of ChlD is essential for complex formation, butmore » some stability is preserved in the absence of the C-terminal integrin domain of ChlD, particularly if the intervening polyproline linker region is retained. Single molecule force spectroscopy (SMFS) was used to determine the factors that stabilize formation of the ChlID–MgADP complex at the single molecule level; ChlD was attached to an atomic force microscope (AFM) probe in two different orientations, and the ChlI subunits were tethered to a silica surface; the probability of subunits interacting more than doubled in the presence of MgADP, and we show that the N-terminal AAA + domain of ChlD mediates this process, in agreement with the microscale thermophoresis data. Analysis of the unbinding data revealed a most probable interaction force of around 109 pN for formation of single ChlID–MgADP complexes. Finally, these experiments provide a quantitative basis for understanding the assembly and function of the Mg chelatase complex.« less

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

Maaloum, M.; Muller, P.; Beker, A-F.

Almost two decades ago, measurements of force versus extension on isolated double-stranded DNA molecules revealed a force plateau. This unusual stretching phenomenon in DNA suggests that the long molecules may be extended from the usual B form into a new conformation. Different models have been proposed to describe the nature of DNA in its stretched form, S-DNA. Using atomic force microscopy combined with a molecular combing method, we identified the structure of {lambda}-phage DNA for different stretching values. We provide strong evidence for the existence of a first-order transition between B form and S form. Beyond a certain extension ofmore » the natural length, DNA molecules adopt a new double-helix conformation characterized by a diameter of 1.2 nm and a helical pitch of18 nm.« less

Iron-embedded C2N monolayer: a promising low-cost and high-activity single-atom catalyst for CO oxidation.

PubMed

He, B L; Shen, J S; Tian, Z X

2016-09-21

An Fe-embedded C2N monolayer as a promising single-atom catalyst for CO oxidation by O2 has been investigated based on first-principles calculations. It is found that the single Fe atom can be strongly trapped in the cavity of the C2N monolayer with a large adsorption energy of 4.55 eV and a high diffusion barrier of at least 3.00 eV to leave the cavity, indicating that Fe should exist in the isolated single-atom form. Due to the localized metal 3d orbitals near the Fermi level, the embedded Fe single-atom catalyst has a high chemical activity for the adsorption of CO and O2 molecules. CO oxidation by O2 on the catalyst would proceed via a two-step mechanism. The first step of the CO oxidation reaction has been studied via the Langmuir-Hinshelwood and Eley-Rideal mechanisms with energy barriers of 0.46 and 0.65 eV, respectively. The second step of the CO oxidation reaction follows the Eley-Rideal mechanism with a much smaller energy barrier of 0.24 eV. For both the steps, the CO2 molecules produced are weakly adsorbed on the substrates, suggesting that the proposed catalyst will not be poisoned by the generated CO2. Our results indicate that the Fe-embedded C2N monolayer is a promising single-atom catalyst for CO oxidation by O2 at low temperatures.

Reconstructing Folding Energy Landscapes by Single-Molecule Force Spectroscopy

PubMed Central

Woodside, Michael T.; Block, Steven M.

2015-01-01

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

Different catalytic effects of a single water molecule: the gas-phase reaction of formic acid with hydroxyl radical in water vapor.

PubMed

Anglada, Josep M; Gonzalez, Javier

2009-12-07

The effect of a single water molecule on the reaction mechanism of the gas-phase reaction between formic acid and the hydroxyl radical was investigated with high-level quantum mechanical calculations using DFT-B3LYP, MP2 and CCSD(T) theoretical approaches in concert with the 6-311+G(2df,2p) and aug-cc-pVTZ basis sets. The reaction between HCOOH and HO has a very complex mechanism involving a proton-coupled electron transfer process (pcet), two hydrogen-atom transfer reactions (hat) and a double proton transfer process (dpt). The hydroxyl radical predominantly abstracts the acidic hydrogen of formic acid through a pcet mechanism. A single water molecule affects each one of these reaction mechanisms in different ways, depending on the way the water interacts. Very interesting is also the fact that our calculations predict that the participation of a single water molecule results in the abstraction of the formyl hydrogen of formic acid through a hydrogen atom transfer process (hat).

DelPhiForce web server: electrostatic forces and energy calculations and visualization.

PubMed

Li, Lin; Jia, Zhe; Peng, Yunhui; Chakravorty, Arghya; Sun, Lexuan; Alexov, Emil

2017-11-15

Electrostatic force is an essential component of the total force acting between atoms and macromolecules. Therefore, accurate calculations of electrostatic forces are crucial for revealing the mechanisms of many biological processes. We developed a DelPhiForce web server to calculate and visualize the electrostatic forces at molecular level. DelPhiForce web server enables modeling of electrostatic forces on individual atoms, residues, domains and molecules, and generates an output that can be visualized by VMD software. Here we demonstrate the usage of the server for various biological problems including protein-cofactor, domain-domain, protein-protein, protein-DNA and protein-RNA interactions. The DelPhiForce web server is available at: http://compbio.clemson.edu/delphi-force. delphi@clemson.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Force-detected nuclear magnetic resonance: recent advances and future challenges.

PubMed

Poggio, M; Degen, C L

2010-08-27

We review recent efforts to detect small numbers of nuclear spins using magnetic resonance force microscopy. Magnetic resonance force microscopy (MRFM) is a scanning probe technique that relies on the mechanical measurement of the weak magnetic force between a microscopic magnet and the magnetic moments in a sample. Spurred by the recent progress in fabricating ultrasensitive force detectors, MRFM has rapidly improved its capability over the last decade. Today it boasts a spin sensitivity that surpasses conventional, inductive nuclear magnetic resonance detectors by about eight orders of magnitude. In this review we touch on the origins of this technique and focus on its recent application to nanoscale nuclear spin ensembles, in particular on the imaging of nanoscale objects with a three-dimensional (3D) spatial resolution better than 10 nm. We consider the experimental advances driving this work and highlight the underlying physical principles and limitations of the method. Finally, we discuss the challenges that must be met in order to advance the technique towards single nuclear spin sensitivity-and perhaps-to 3D microscopy of molecules with atomic resolution.

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

DOE PAGES

Cortini, Ruggero; Cheng, Xiaolin; Smith, Jeremy C.

2017-01-16

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

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

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

Cortini, Ruggero; Cheng, Xiaolin; Smith, Jeremy C.

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

ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc05720a Click here for additional data file.

PubMed Central

Smith, J. S.

2017-01-01

Deep learning is revolutionizing many areas of science and technology, especially image, text, and speech recognition. In this paper, we demonstrate how a deep neural network (NN) trained on quantum mechanical (QM) DFT calculations can learn an accurate and transferable potential for organic molecules. We introduce ANAKIN-ME (Accurate NeurAl networK engINe for Molecular Energies) or ANI for short. ANI is a new method designed with the intent of developing transferable neural network potentials that utilize a highly-modified version of the Behler and Parrinello symmetry functions to build single-atom atomic environment vectors (AEV) as a molecular representation. AEVs provide the ability to train neural networks to data that spans both configurational and conformational space, a feat not previously accomplished on this scale. We utilized ANI to build a potential called ANI-1, which was trained on a subset of the GDB databases with up to 8 heavy atoms in order to predict total energies for organic molecules containing four atom types: H, C, N, and O. To obtain an accelerated but physically relevant sampling of molecular potential surfaces, we also proposed a Normal Mode Sampling (NMS) method for generating molecular conformations. Through a series of case studies, we show that ANI-1 is chemically accurate compared to reference DFT calculations on much larger molecular systems (up to 54 atoms) than those included in the training data set. PMID:28507695

Hydrophobic Hydration of Stimulus-Responsive Polyproteins Measured by Single Molecule Force Spectroscopy

NASA Astrophysics Data System (ADS)

Zauscher, Stefan

2007-03-01

We present a new procedure to reduce and analyze force-extension data obtained by single molecule force spectroscopy (SMFS). This approach allows, for the first time, to infer effects of solvent quality and minor changes in molecular architecture on molecular-elasticity of individual (bio)macromolecules. Specifically, we show how changes in the effective Kuhn segment length can be used to interpret the hydrophobic hydration behavior of elastin-like polypeptides (ELPs).Our results are intriguing as they suggest that SMFS in combination with our analysis procedure can be used to study the subtleties of polypeptide-water interactions on the single molecule level. We also report on the force-induced cis-trans isomerization of prolines, which are repeated every fifth residue in the main chain of ELPs. We present evidence for this mechanism by Monte Carlo simulations of the force-extension curves using an elastically coupled two-state system. Our results suggest that SMFS could be used to assay proline cis-trans isomerization in proteins and may thus have significant potential diagnostic utility.

Single-molecule designs for electric switches and rectifiers.

PubMed

Kornilovitch, Pavel; Bratkovsky, Alexander; Williams, Stanley

2003-12-01

A design for molecular rectifiers is proposed. Current rectification is based on the spatial asymmetry of a molecule and requires only one resonant conducting molecular orbital. Rectification is caused by asymmetric coupling of the orbital to the electrodes, which results in asymmetric movement of the two Fermi levels with respect to the orbital under external bias. Results from numerical studies of the family of suggested molecular rectifiers, HS-(CH(2))(n)-C(6)H(4)(CH(2))(m)SH, are presented. Current rectification ratios in excess of 100 are achievable for n = 2 and m > 6. A class of bistable stator-rotor molecules is proposed. The stationary part connects the two electrodes and facilitates electron transport between them. The rotary part, which has a large dipole moment, is attached to an atom of the stator via a single sigma bond. Electrostatic bonds formed between the oxygen atom of the rotor and hydrogen atoms of the stator make the symmetric orientation of the dipole unstable. The rotor has two potential minima with equal energy for rotation about the sigma bond. The dipole can be flipped between the two states by an external electric field. Both rotor-orientation states have asymmetric current-voltage characteristics that are the reverse of each other, so they are distinguishable electrically. Theoretical results on conformation, energy barriers, retention times, switching voltages, and current-voltage characteristics are presented for a particular stator-rotor molecule. Such molecules could be the base for single-molecule switches, reversible diodes, and other molecular electronic devices.

Interacting dark resonances with plasmonic meta-molecules

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

Jha, Pankaj K.; Mrejen, Michael; Kim, Jeongmin

2014-09-15

Dark state physics has led to a variety of remarkable phenomena in atomic physics, quantum optics, and information theory. Here, we investigate interacting dark resonance type physics in multi-layered plasmonic meta-molecules. We theoretically demonstrate that these plasmonic meta-molecules exhibit sub-natural spectral response, analogous to conventional atomic four-level configuration, by manipulating the evanescent coupling between the bright and dark elements (plasmonic atoms). Using cascaded coupling, we show nearly 4-fold reduction in linewidth of the hybridized resonance compared to a resonantly excited single bright plasmonic atom with same absorbance. In addition, we engineered the geometry of the meta-molecules to realize efficient intramolecularmore » excitation transfer with nearly 80%, on resonant excitation, of the total absorption being localized at the second dark plasmonic atom. An analytical description of the spectral response of the structure is presented with full electrodynamics simulations to corroborate our results. Such multilayered meta-molecules can bring a new dimension to higher quality factor plasmonic resonance, efficient excitation transfer, wavelength demultiplexing, and enhanced non-linearity at nanoscale.« less

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

DOE PAGES

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

2015-06-04

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

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

PubMed Central

2015-01-01

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

Building one molecule from a reservoir of two atoms.

PubMed

Liu, L R; Hood, J D; Yu, Y; Zhang, J T; Hutzler, N R; Rosenband, T; Ni, K-K

2018-05-25

Chemical reactions typically proceed via stochastic encounters between reactants. Going beyond this paradigm, we combined exactly two atoms in a single, controlled reaction. The experimental apparatus traps two individual laser-cooled atoms [one sodium (Na) and one cesium (Cs)] in separate optical tweezers and then merges them into one optical dipole trap. Subsequently, photoassociation forms an excited-state NaCs molecule. The discovery of previously unseen resonances near the molecular dissociation threshold and measurement of collision rates are enabled by the tightly trapped ultracold sample of atoms. As laser-cooling and trapping capabilities are extended to more elements, the technique will enable the study of more diverse, and eventually more complex, molecules in an isolated environment, as well as synthesis of designer molecules for qubits. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Controlling single-molecule junction conductance by molecular interactions

NASA Astrophysics Data System (ADS)

Kitaguchi, Y.; Habuka, S.; Okuyama, H.; Hatta, S.; Aruga, T.; Frederiksen, T.; Paulsson, M.; Ueba, H.

2015-07-01

For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment.

Dielectrophoretic immobilization of proteins: Quantification by atomic force microscopy.

PubMed

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

2015-09-01

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

Vertebrate Membrane Proteins: Structure, Function, and Insights from Biophysical Approaches

PubMed Central

MÜLLER, DANIEL J.; WU, NAN; PALCZEWSKI, KRZYSZTOF

2008-01-01

Membrane proteins are key targets for pharmacological intervention because they are vital for cellular function. Here, we analyze recent progress made in the understanding of the structure and function of membrane proteins with a focus on rhodopsin and development of atomic force microscopy techniques to study biological membranes. Membrane proteins are compartmentalized to carry out extra- and intracellular processes. Biological membranes are densely populated with membrane proteins that occupy approximately 50% of their volume. In most cases membranes contain lipid rafts, protein patches, or paracrystalline formations that lack the higher-order symmetry that would allow them to be characterized by diffraction methods. Despite many technical difficulties, several crystal structures of membrane proteins that illustrate their internal structural organization have been determined. Moreover, high-resolution atomic force microscopy, near-field scanning optical microscopy, and other lower resolution techniques have been used to investigate these structures. Single-molecule force spectroscopy tracks interactions that stabilize membrane proteins and those that switch their functional state; this spectroscopy can be applied to locate a ligand-binding site. Recent development of this technique also reveals the energy landscape of a membrane protein, defining its folding, reaction pathways, and kinetics. Future development and application of novel approaches during the coming years should provide even greater insights to the understanding of biological membrane organization and function. PMID:18321962

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

PubMed

Torres, Edmanuel; DiLabio, Gino A

2013-08-13

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

Method for preparation and readout of polyatomic molecules in single quantum states

NASA Astrophysics Data System (ADS)

Patterson, David

2018-03-01

Polyatomic molecular ions contain many desirable attributes of a useful quantum system, including rich internal degrees of freedom and highly controllable coupling to the environment. To date, the vast majority of state-specific experimental work on molecular ions has concentrated on diatomic species. The ability to prepare and read out polyatomic molecules in single quantum states would enable diverse experimental avenues not available with diatomics, including new applications in precision measurement, sensitive chemical and chiral analysis at the single-molecule level, and precise studies of Hz-level molecular tunneling dynamics. While cooling the motional state of a polyatomic ion via sympathetic cooling with a laser-cooled atomic ion is straightforward, coupling this motional state to the internal state of the molecule has proven challenging. Here we propose a method for readout and projective measurement of the internal state of a trapped polyatomic ion. The method exploits the rich manifold of technically accessible rotational states in the molecule to realize robust state preparation and readout with far less stringent engineering than quantum logic methods recently demonstrated on diatomic molecules. The method can be applied to any reasonably small (≲10 atoms) polyatomic ion with an anisotropic polarizability.

Effects of the molecule-electrode interface on the low-bias conductance of Cu–H{sub 2}–Cu single-molecule junctions

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

Jiang, Zhuoling; Centre for Nanoscale Science and Technology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871; Wang, Hao

The atomic structure and electronic transport properties of a single hydrogen molecule connected to both symmetric and asymmetric Cu electrodes are investigated by using the non-equilibrium Green’s function formalism combined with the density functional theory. Our calculations show that in symmetric Cu–H{sub 2}–Cu junctions, the low-bias conductance drops rapidly upon stretching, while asymmetric ones present a low-bias conductance spanning the 0.2–0.3 G{sub 0} interval for a wide range of electrode separations. This is in good agreement with experiments on Cu atomic contacts in a hydrogen environment. Furthermore, the distribution of the calculated vibrational energies of the two hydrogen atoms inmore » the asymmetric Cu–H{sub 2}–Cu junction is also consistent with experiments. These findings provide clear evidence for the formation of asymmetric Cu–H{sub 2}–Cu molecular junctions in breaking Cu atomic contacts in the presence of hydrogen and are also helpful for the design of molecular devices with Cu electrodes.« less

Kinetics of molecular transitions with dynamic disorder in single-molecule pulling experiments

NASA Astrophysics Data System (ADS)

Zheng, Yue; Li, Ping; Zhao, Nanrong; Hou, Zhonghuai

2013-05-01

Macromolecular transitions are subject to large fluctuations of rate constant, termed as dynamic disorder. The individual or intrinsic transition rates and activation free energies can be extracted from single-molecule pulling experiments. Here we present a theoretical framework based on a generalized Langevin equation with fractional Gaussian noise and power-law memory kernel to study the kinetics of macromolecular transitions to address the effects of dynamic disorder on barrier-crossing kinetics under external pulling force. By using the Kramers' rate theory, we have calculated the fluctuating rate constant of molecular transition, as well as the experimentally accessible quantities such as the force-dependent mean lifetime, the rupture force distribution, and the speed-dependent mean rupture force. Particular attention is paid to the discrepancies between the kinetics with and without dynamic disorder. We demonstrate that these discrepancies show strong and nontrivial dependence on the external force or the pulling speed, as well as the barrier height of the potential of mean force. Our results suggest that dynamic disorder is an important factor that should be taken into account properly in accurate interpretations of single-molecule pulling experiments.

[Single-molecule detection and characterization of DNA replication based on DNA origami].

PubMed

Wang, Qi; Fan, Youjie; Li, Bin

2014-08-01

To investigate single-molecule detection and characterization of DNA replication. Single-stranded DNA (ssDNA) as the template of DNA replication was attached to DNA origami by a hybridization reaction based on the complementary base-pairing principle. DNA replication catalyzed by E.coli DNA polymerase I Klenow Fragment (KF) was detected using atomic force microscopy (AFM). The height variations between the ssDNA and the double-stranded DNA (dsDNA), the distribution of KF during DNA replication and biotin-streptavidin (BA) complexes on the DNA strand after replication were detected. Agarose gel electrophoresis was employed to analyze the changes in the DNA after replication. The designed ssDNA could be anchored on the target positions of over 50% of the DNA origami. The KF was capable of binding to the ssDNA fixed on DNA origami and performing its catalytic activities, and was finally dissociated from the DNA after replication. The height of DNA strand increased by about 0.7 nm after replication. The addition of streptavidin also resulted in an DNA height increase to about 4.9 nm due to the formation of BA complexes on the biotinylated dsDNA. The resulting dsDNA and BA complex were subsequently confirmed by agarose gel electrophoresis. The combination of AFM and DNA origami allows detection and characterization of DNA replication at the single molecule level, and this approach provides better insights into the mechanism of DNA polymerase and the factors affecting DNA replication.

Direct observation and control of hydrogen-bond dynamics using low-temperature scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Kumagai, Takashi

2015-08-01

Hydrogen(H)-bond dynamics are involved in many elementary processes in chemistry and biology. Because of its fundamental importance, a variety of experimental and theoretical approaches have been employed to study the dynamics in gas, liquid, solid phases, and their interfaces. This review describes the recent progress of direct observation and control of H-bond dynamics in several model systems on a metal surface by using low-temperature scanning tunneling microscopy (STM). General aspects of H-bond dynamics and the experimental methods are briefly described in chapter 1 and 2. In the subsequent four chapters, I present direct observation of an H-bond exchange reaction within a single water dimer (chapter 3), a symmetric H bond (chapter 4) and H-atom relay reactions (chapter 5) within water-hydroxyl complexes, and an intramolecular H-atom transfer reaction (tautomerization) within a single porphycene molecule (chapter 6). These results provide novel microscopic insights into H-bond dynamics at the single-molecule level, and highlight significant impact on the process from quantum effects, namely tunneling and zero-point vibration, resulting from the small mass of H atom. Additionally, local environmental effect on H-bond dynamics is also examined by using atom/molecule manipulation with the STM.

Towards force spectroscopy of single tip-link bonds

NASA Astrophysics Data System (ADS)

Koussa, Mounir A.; Sotomayor, Marcos; Wong, Wesley P.; Corey, David P.

2015-12-01

Inner-ear mechanotransduction relies on tip links, fine protein filaments made of cadherin-23 and protocadherin-15 that convey tension to mechanosensitive channels at the tips of hair-cell stereocilia. The tip-link cadherins are thought to form a heterotetrameric complex, with two cadherin-23 molecules forming the upper part of the filament and two protocadherin-15 molecules forming the lower end. The interaction between cadherin-23 and protocadherin-15 is mediated by their N-terminal tips. Missense mutations that modify the interaction interface impair binding and lead to deafness. Molecular dynamics simulations predict that the tip-link bond is mechanically strong enough to withstand forces in hair cells, but its experimentally determined strength is unknown. We have developed molecular tools to facilitate single-molecule force spectroscopy on the tip link bond. Self-assembling DNA nanoswitches are functionalized with the interacting tips of cadherin-23 and protocadherin-15 using the enzyme sortase under conditions that preserve protein function. These tip link nanoswitches are designed to provide a signature force-extension profile. This molecular signature should allow us to identify single-molecule rupture events in pulling experiments.

Low-affinity binding in cis to P2Y2R mediates force-dependent integrin activation during hantavirus infection

PubMed Central

Bondu, Virginie; Wu, Chenyu; Cao, Wenpeng; Simons, Peter C.; Gillette, Jennifer; Zhu, Jieqing; Erb, Laurie; Zhang, X. Frank; Buranda, Tione

2017-01-01

Pathogenic hantaviruses bind to the plexin-semaphorin-integrin (PSI) domain of inactive, β3 integrins. Previous studies have implicated a cognate cis interaction between the bent conformation β5/β3 integrins and an arginine-glycine-aspartic acid (RGD) sequence in the first extracellular loop of P2Y2R. With single-molecule atomic force microscopy, we show a specific interaction between an atomic force microscopy tip decorated with recombinant αIIbβ3 integrins and (RGD)P2Y2R expressed on cell membranes. Mutation of the RGD sequence to RGE in the P2Y2R removes this interaction. Binding of inactivated and fluorescently labeled Sin Nombre virus (SNV) to the integrin PSI domain stimulates higher affinity for (RGD)P2Y2R on cells, as measured by an increase in the unbinding force. In CHO cells, stably expressing αIIbβ3 integrins, virus engagement at the integrin PSI domain, recapitulates physiologic activation of the integrin as indicated by staining with the activation-specific mAB PAC1. The data also show that blocking of the Gα13 protein from binding to the cytoplasmic domain of the β3 integrin prevents outside-in signaling and infection. We propose that the cis interaction with P2Y2R provides allosteric resistance to the membrane-normal motion associated with the switchblade model of integrin activation, where the development of tensile force yields physiological integrin activation. PMID:28835374

Quantitative single molecule measurements on the interaction forces of poly(L-glutamic acid) with calcite crystals.

PubMed

Sonnenberg, Lars; Luo, Yufei; Schlaad, Helmut; Seitz, Markus; Cölfen, Helmut; Gaub, Hermann E

2007-12-12

The interaction between poly(L-glutamic acid) (PLE) and calcite crystals was studied with AFM-based single molecule force spectroscopy. Block copolymers of poly(ethylene oxide) (PEO) and PLE were synthesized and covalently attached to the tip of an AFM cantilever. In desorption measurements the molecules were allowed to adsorb on the calcite crystal faces and afterward successively desorbed. The corresponding desorption forces were detected with high precision, showing for example a force transition between the two blocks. Because of its importance in the crystallization process in biominerals, the PLE-calcite interaction was investigated as a function of the pH as well as the calcium concentration of the aqueous solution. The sensitivity of the technique was underlined by resolving different interaction forces for calcite (104) and calcite (100).

Performing the Millikan experiment at the molecular scale: Determination of atomic Millikan-Thomson charges by computationally measuring atomic forces.

PubMed

Rogers, T Ryan; Wang, Feng

2017-10-28

An atomic version of the Millikan oil drop experiment is performed computationally. It is shown that for planar molecules, the atomic version of the Millikan experiment can be used to define an atomic partial charge that is free from charge flow contributions. We refer to this charge as the Millikan-Thomson (MT) charge. Since the MT charge is directly proportional to the atomic forces under a uniform electric field, it is the most relevant charge for force field developments. The MT charge shows good stability with respect to different choices of the basis set. In addition, the MT charge can be easily calculated even at post-Hartree-Fock levels of theory. With the MT charge, it is shown that for a planar water dimer, the charge transfer from the proton acceptor to the proton donor is about -0.052 e. While both planar hydrated cations and anions show signs of charge transfer, anions show a much more significant charge transfer to the hydration water than the corresponding cations. It might be important to explicitly model the ion charge transfer to water in a force field at least for the anions.

Probing the Structure and Dynamics of Interfacial Water with Scanning Tunneling Microscopy and Spectroscopy.

PubMed

Guo, Jing; You, Sifan; Wang, Zhichang; Peng, Jinbo; Ma, Runze; Jiang, Ying

2018-05-27

Water/solid interfaces are ubiquitous and play a key role in many environmental, biophysical, and technological processes. Resolving the internal structure and probing the hydrogen-bond (H-bond) dynamics of the water molecules adsorbed on solid surfaces are fundamental issues of water science, which remains a great challenge owing to the light mass and small size of hydrogen. Scanning tunneling microscopy (STM) is a promising tool for attacking these problems, thanks to its capabilities of sub-Ångström spatial resolution, single-bond vibrational sensitivity, and atomic/molecular manipulation. The designed experimental system consists of a Cl-terminated tip and a sample fabricated by dosing water molecules in situ onto the Au(111)-supported NaCl(001) surfaces. The insulating NaCl films electronically decouple the water from the metal substrates, so the intrinsic frontier orbitals of water molecules are preserved. The Cl-tip facilitates the manipulation of the single water molecules, as well as gating the orbitals of water to the proximity of Fermi level (EF) via tip-water coupling. This paper outlines the detailed methods of submolecular resolution imaging, molecular/atomic manipulation, and single-bond vibrational spectroscopy of interfacial water. These studies open up a new route for investigating the H-bonded systems at the atomic scale.

High-spatial-resolution mapping of catalytic reactions on single particles

DOE PAGES

Wu, Chung-Yeh; Wolf, William J.; Levartovsky, Yehonatan; ...

2017-01-26

We report the critical role in surface reactions and heterogeneous catalysis of metal atoms with low coordination numbers, such as found at atomic steps and surface defects, is firmly established. But despite the growing availability of tools that enable detailed in situ characterization, so far it has not been possible to document this role directly. Surface properties can be mapped with high spatial resolution, and catalytic conversion can be tracked with a clear chemical signature; however, the combination of the two, which would enable high-spatial-resolution detection of reactions on catalytic surfaces, has rarely been achieved. Single-molecule fluorescence spectroscopy has beenmore » used to image and characterize single turnover sites at catalytic surfaces, but is restricted to reactions that generate highly fluorescing product molecules. Herein the chemical conversion of N-heterocyclic carbene molecules attached to catalytic particles is mapped using synchrotron-radiation-based infrared nanospectroscopy with a spatial resolution of 25 nanometres, which enabled particle regions that differ in reactivity to be distinguished. Lastly, these observations demonstrate that, compared to the flat regions on top of the particles, the peripheries of the particles-which contain metal atoms with low coordination numbers-are more active in catalysing oxidation and reduction of chemically active groups in surface-anchored N-heterocyclic carbene molecules.« less

Inorganic and Organometallic Molecular Wires for Single-Molecule Devices.

PubMed

Tanaka, Yuya; Kiguchi, Manabu; Akita, Munetaka

2017-04-06

Recent developments of single-molecule conductance measurements allow us to understand fundamental conducting properties of molecular wires. While a wide variety of organic molecular wires have been studied so far, inorganic and organometallic molecular wires have received much less attention. However, molecular wires with transition-metal atoms show interesting features and functions distinct from those of organic wires. These properties originate mainly from metal-ligand dπ-pπ interactions and metal-metal d-d interactions. Thanks to the rich combination of metal atoms and supporting ligands, frontier orbital energies of the molecular wires can be finely tuned to lead to highly conducting molecular wires. Moreover, the unique electronic structures of metal complexes are susceptible to subtle environmental changes, leading to potential functional molecular devices. This article reviews recent advances in the single-molecule conductance study of inorganic and organometallic molecular wires. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Applications of atomic force microscopy to the studies of biomaterials in biomolecular systems

NASA Astrophysics Data System (ADS)

Ma, Xiang

Atomic force microscopy (AFM) is a unique tool for the studies of nanoscale structures and interactions. In this dissertation, I applied AFM to study transitions among multiple states of biomaterials in three different microscopic biomolecular systems: MukB-dependent DNA condensation, holdfast adhesion, and virus elasticity. To elucidate the mechanism of MukB-dependent DNA condensation, I have studied the conformational changes of MukB proteins as indicators for the strength of interactions between MukB, DNA and other molecular factors, such as magnesium and ParC proteins, using high-resolution AFM imaging. To determine the physical origins of holdfast adhesion, I have investigated the dynamics of adhesive force development of the holdfast, employing AFM force spectroscopy. By measuring rupture forces between the holdfast and the substrate, I showed that the holdfast adhesion is strongly time-dependent and involves transformations at multiple time scales. Understanding the mechanisms of adhesion force development of the holdfast will be critical for future engineering of holdfasts properties for various applications. Finally, I have examined the elasticity of self-assembled hepatitis B virus-like particles (HBV VLPs) and brome mosaic virus (BMV) in response to changes of pH and salinity, using AFM nanoindentation. The distributions of elasticity were mapped on a single particle level and compared between empty, RNA- and gold-filled HBV VLPs. I found that a single HBV VLP showed heterogeneous distribution of elasticity and a two-step buckling transition, suggesting a discrete property of HBV capsids. For BMV, I have showed that viruses containing different RNA molecules can be distinguished by mechanical measurements, while they are indistinguishable by morphology. I also studied the effect of pH on the elastic behaviors of three-particle BMV and R3/4 BMV. This study can yield insights into RNA presentation/release mechanisms, and could help us to design novel drug delivery vehicles.

Nanomechanics of Yeast Surfaces Revealed by AFM

NASA Astrophysics Data System (ADS)

Dague, Etienne; Beaussart, Audrey; Alsteens, David

Despite the large and well-documented characterization of the microbial cell wall in terms of chemical composition, the determination of the mechanical properties of surface molecules in relation to their function remains a key challenge in cell biology.The emergence of powerful tools allowing molecular manipulations has already revolutionized our understanding of the surface properties of fungal cells. At the frontier between nanophysics and molecular biology, atomic force microscopy (AFM), and more specifically single-molecule force spectroscopy (SMFS), has strongly contributed to our current knowledge of the cell wall organization and nanomechanical properties. However, due to the complexity of the technique, measurements on live cells are still at their infancy.In this chapter, we describe the cell wall composition and recapitulate the principles of AFM as well as the main current methodologies used to perform AFM measurements on live cells, including sample immobilization and tip functionalization.The current status of the progress in probing nanomechanics of the yeast surface is illustrated through three recent breakthrough studies. Determination of the cell wall nanostructure and elasticity is presented through two examples: the mechanical response of mannoproteins from brewing yeasts and elasticity measurements on lacking polysaccharide mutant strains. Additionally, an elegant study on force-induced unfolding and clustering of adhesion proteins located at the cell surface is also presented.

Evidence that αC region is origin of low modulus, high extensibility, and strain stiffening in fibrin fibers.

PubMed

Houser, John R; Hudson, Nathan E; Ping, Lifang; O'Brien, E Timothy; Superfine, Richard; Lord, Susan T; Falvo, Michael R

2010-11-03

Fibrin fibers form the structural scaffold of blood clots and perform the mechanical task of stemming blood flow. Several decades of investigation of fibrin fiber networks using macroscopic techniques have revealed remarkable mechanical properties. More recently, the microscopic origins of fibrin's mechanics have been probed through direct measurements on single fibrin fibers and individual fibrinogen molecules. Using a nanomanipulation system, we investigated the mechanical properties of individual fibrin fibers. The fibers were stretched with the atomic force microscope, and stress-versus-strain data was collected for fibers formed with and without ligation by the activated transglutaminase factor XIII (FXIIIa). We observed that ligation with FXIIIa nearly doubled the stiffness of the fibers. The stress-versus-strain behavior indicates that fibrin fibers exhibit properties similar to other elastomeric biopolymers. We propose a mechanical model that fits our observed force extension data, is consistent with the results of the ligation data, and suggests that the large observed extensibility in fibrin fibers is mediated by the natively unfolded regions of the molecule. Although some models attribute fibrin's force-versus-extension behavior to unfolding of structured regions within the monomer, our analysis argues that these models are inconsistent with the measured extensibility and elastic modulus. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Mapping HA-tagged protein at the surface of living cells by atomic force microscopy.

PubMed

Formosa, C; Lachaize, V; Galés, C; Rols, M P; Martin-Yken, H; François, J M; Duval, R E; Dague, E

2015-01-01

Single-molecule force spectroscopy using atomic force microscopy (AFM) is more and more used to detect and map receptors, enzymes, adhesins, or any other molecules at the surface of living cells. To be specific, this technique requires antibodies or ligands covalently attached to the AFM tip that can specifically interact with the protein of interest. Unfortunately, specific antibodies are usually lacking (low affinity and specificity) or are expensive to produce (monoclonal antibodies). An alternative strategy is to tag the protein of interest with a peptide that can be recognized with high specificity and affinity with commercially available antibodies. In this context, we chose to work with the human influenza hemagglutinin (HA) tag (YPYDVPDYA) and labeled two proteins: covalently linked cell wall protein 12 (Ccw12) involved in cell wall remodeling in the yeast Saccharomyces cerevisiae and the β2-adrenergic receptor (β2-AR), a G protein-coupled receptor (GPCR) in higher eukaryotes. We first described the interaction between HA antibodies, immobilized on AFM tips, and HA epitopes, immobilized on epoxy glass slides. Using our system, we then investigated the distribution of Ccw12 proteins over the cell surface of the yeast S. cerevisiae. We were able to find the tagged protein on the surface of mating yeasts, at the tip of the mating projections. Finally, we could unfold multimers of β2-AR from the membrane of living transfected chinese hamster ovary cells. This result is in agreement with GPCR oligomerization in living cell membranes and opens the door to the study of the influence of GPCR ligands on the oligomerization process. Copyright © 2014 John Wiley & Sons, Ltd.

How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?

PubMed

Šponer, Jiří; Krepl, Miroslav; Banáš, Pavel; Kührová, Petra; Zgarbová, Marie; Jurečka, Petr; Havrila, Marek; Otyepka, Michal

2017-05-01

We provide a critical assessment of explicit-solvent atomistic molecular dynamics (MD) simulations of RNA and protein/RNA complexes, written primarily for non-specialists with an emphasis to explain the limitations of MD. MD simulations can be likened to hypothetical single-molecule experiments starting from single atomistic conformations and investigating genuine thermal sampling of the biomolecules. The main advantage of MD is the unlimited temporal and spatial resolution of positions of all atoms in the simulated systems. Fundamental limitations are the short physical time-scale of simulations, which can be partially alleviated by enhanced-sampling techniques, and the highly approximate atomistic force fields describing the simulated molecules. The applicability and present limitations of MD are demonstrated on studies of tetranucleotides, tetraloops, ribozymes, riboswitches and protein/RNA complexes. Wisely applied simulations respecting the approximations of the model can successfully complement structural and biochemical experiments. WIREs RNA 2017, 8:e1405. doi: 10.1002/wrna.1405 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

Illusory spirals and loops in crystal growth

PubMed Central

Shtukenberg, Alexander G.; Zhu, Zina; Bhandari, Misha; Song, Pengcheng; Kahr, Bart; Ward, Michael D.

2013-01-01

The theory of dislocation-controlled crystal growth identifies a continuous spiral step with an emergent lattice displacement on a crystal surface; a mechanistic corollary is that closely spaced, oppositely winding spirals merge to form concentric loops. In situ atomic force microscopy of step propagation on pathological l-cystine crystals did indeed show spirals and islands with step heights of one lattice displacement. We show by analysis of the rates of growth of smaller steps only one molecule high that the major morphological spirals and loops are actually consequences of the bunching of the smaller steps. The morphology of the bunched steps actually inverts the predictions of the theory: Spirals arise from pairs of dislocations, loops from single dislocations. Only through numerical simulation of the growth is it revealed how normal growth of anisotropic layers of molecules within the highly symmetrical crystals can conspire to create features in apparent violation of the classic theory. PMID:24101507

Sequence-dependent folding landscapes of adenine riboswitch aptamers.

PubMed

Lin, Jong-Chin; Hyeon, Changbong; Thirumalai, D

2014-04-14

Expression of a large fraction of genes in bacteria is controlled by riboswitches, which are found in the untranslated region of mRNA. Structurally riboswitches have a conserved aptamer domain to which a metabolite binds, resulting in a conformational change in the downstream expression platform. Prediction of the functions of riboswitches requires a quantitative description of the folding landscape so that the barriers and time scales for the conformational change in the switching region in the aptamer can be estimated. Using a combination of all atom molecular dynamics (MD) and coarse-grained model simulations we studied the response of adenine (A) binding add and pbuE A-riboswitches to mechanical force. The two riboswitches contain a structurally similar three-way junction formed by three paired helices, P1, P2, and P3, but carry out different functions. Using pulling simulations, with structures generated in MD simulations, we show that after P1 rips the dominant unfolding pathway in the add A-riboswitch is the rupture of P2 followed by unraveling of P3. In the pbuE A-riboswitch, after P1 unfolds P3 ruptures ahead of P2. The order of unfolding of the helices, which is in accord with single molecule pulling experiments, is determined by the relative stabilities of the individual helices. Our results show that the stability of isolated helices determines the order of assembly and response to force in these non-coding regions. We use the simulated free energy profile for the pbuE A-riboswitch to estimate the time scale for allosteric switching, which shows that this riboswitch is under kinetic control lending additional support to the conclusion based on single molecule pulling experiments. A consequence of the stability hypothesis is that a single point mutation (U28C) in the P2 helix of the add A-riboswitch, which increases the stability of P2, would make the folding landscapes of the two riboswitches similar. This prediction can be tested in single molecule pulling experiments.

The effect of defects on the catalytic activity of single Au atom supported carbon nanotubes and reaction mechanism for CO oxidation.

PubMed

Ali, Sajjad; Fu Liu, Tian; Lian, Zan; Li, Bo; Sheng Su, Dang

2017-08-23

The mechanism of CO oxidation by O 2 on a single Au atom supported on pristine, mono atom vacancy (m), di atom vacancy (di) and the Stone Wales defect (SW) on single walled carbon nanotube (SWCNT) surface is systematically investigated theoretically using density functional theory. We determine that single Au atoms can be trapped effectively by the defects on SWCNTs. The defects on SWCNTs can enhance both the binding strength and catalytic activity of the supported single Au atom. Fundamental aspects such as adsorption energy and charge transfer are elucidated to analyze the adsorption properties of CO and O 2 and co-adsorption of CO and O 2 molecules. It is found that CO binds stronger than O 2 on Au supported SWCNT. We clearly demonstrate that the defected SWCNT surface promotes electron transfer from the supported single Au atom to O 2 molecules. On the other hand, this effect is weaker for pristine SWCNTs. It is observed that the high density of spin-polarized states are localized in the region of the Fermi level due to the strong interactions between Au (5d orbital) and the adjacent carbon (2p orbital) atoms, which influence the catalytic performance. In addition, we elucidate both the Langmuir-Hinshelwood (LH) and Eley-Rideal (ER) mechanisms of CO oxidation by O 2 . For the LH pathway, the barriers of the rate-limiting step are calculated to be 0.02 eV and 0.05 eV for Au/m-SWCNT and Au/di-SWCNT, respectively. To regenerate the active sites, an ER-like reaction occurs to form a second CO 2 molecule. The ER pathway is observed on Au/m-SWCNT, Au/SW-SWCNT and Au/SWCNT in which the Au/m-SWCNT has a smaller barrier. The comparison with a previous study (Lu et al., J. Phys. Chem. C, 2009, 113, 20156-20160.) indicates that the curvature effect of SWCNTs is important for the catalytic property of the supported single Au. Overall, Au/m-SWCNT is identified as the most active catalyst for CO oxidation compared to pristine SWCNT, SW-SWCNT and di-SWCNT. Our findings give a clear description on the relationship between the defects in the support and the catalytic properties of Au and open a new avenue to develop carbon nanomaterial-based single atom catalysts for application in environmental and energy related fields.

Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches.

PubMed

Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W

2016-08-25

Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and the pairwise-atomic Hamiltonian matrices required for practical applications. These matrices can be retained as functions of scalar atomic-pair separations and employed in assembling aggregate Hamiltonian matrices, with Wigner rotation matrices providing analytical representations of their angular degrees of freedom. In this way, ab initio potential energy surfaces are obtained in the complete absence of repeated evaluations and transformations of the one- and two-electron integrals at different molecular geometries required in most ab inito molecular calculations, with large Hamiltonian matrix assembly simplified and explicit diagonalizations avoided employing partitioning and Brillouin-Wigner or Rayleigh-Schrödinger perturbation theory. Illustrative applications of the important components of the formalism, selected aspects of the scaling of the approach, and aspects of "on-the-fly" interfaces with Monte Carlo and molecular-dynamics methods are described in anticipation of subsequent applications to biomolecules and other large aggregates.

A multiplexed magnetic tweezer with precision particle tracking and bi-directional force control.

PubMed

Johnson, Keith C; Clemmens, Emilie; Mahmoud, Hani; Kirkpatrick, Robin; Vizcarra, Juan C; Thomas, Wendy E

2017-01-01

In the past two decades, methods have been developed to measure the mechanical properties of single biomolecules. One of these methods, Magnetic tweezers, is amenable to aquisition of data on many single molecules simultaneously, but to take full advantage of this "multiplexing" ability, it is necessary to simultaneously incorprorate many capabilities that ahve been only demonstrated separately. Our custom built magnetic tweezer combines high multiplexing, precision bead tracking, and bi-directional force control into a flexible and stable platform for examining single molecule behavior. This was accomplished using electromagnets, which provide high temporal control of force while achieving force levels similar to permanent magnets via large paramagnetic beads. Here we describe the instrument and its ability to apply 2-260 pN of force on up to 120 beads simultaneously, with a maximum spatial precision of 12 nm using a variety of bead sizes and experimental techniques. We also demonstrate a novel method for increasing the precision of force estimations on heterogeneous paramagnetic beads using a combination of density separation and bi-directional force correlation which reduces the coefficient of variation of force from 27% to 6%. We then use the instrument to examine the force dependence of uncoiling and recoiling velocity of type 1 fimbriae from Eschericia coli ( E. coli ) bacteria, and see similar results to previous studies. This platform provides a simple, effective, and flexible method for efficiently gathering single molecule force spectroscopy measurements.

Detecting molecules and cells labeled with magnetic particles using an atomic magnetometer

NASA Astrophysics Data System (ADS)

Yu, Dindi; Ruangchaithaweesuk, Songtham; Yao, Li; Xu, Shoujun

2012-09-01

The detection of magnetically labeled molecules and cells involves three essential parameters: sensitivity, spatial resolution, and molecular specificity. We report on the use of atomic magnetometry and its derivative techniques to achieve high performance in terms of all these parameters. With a sensitivity of 80 fT/√Hz for dc magnetic fields, we show that 7,000 streptavidin-conjugated magnetic microparticles magnetized by a permanent magnet produce a magnetic field of 650 pT; this result predicts that a single such particle can be detected during one second of signal averaging. Spatial information is obtained using a scanning magnetic imaging scheme. The spatial resolution is 20 μm with a detection distance of more than 1 cm; this distance is much longer than that in previous reports. The molecular specificity is achieved using force-induced remnant magnetization spectroscopy, which currently uses an atomic magnetometer for detection. As an example, we perform measurement of magnetically labeled human CD4+ T cells, whose count in the blood is the diagnostic criterion for human immunodeficiency virus infection. Magnetic particles that are specifically bound to the cells are resolved from nonspecifically bound particles and quantitatively correlate with the number of cells. The magnetic particles have an overall size of 2.8 μm, with a magnetic core in nanometer regime. The combination of our techniques is predicted to be useful in molecular and cellular imaging.

Azobenzenes as light-controlled molecular electronic switches in nanoscale metal-molecule-metal junctions.

PubMed

Mativetsky, Jeffrey M; Pace, Giuseppina; Elbing, Mark; Rampi, Maria A; Mayor, Marcel; Samorì, Paolo

2008-07-23

Conductance switching associated with the photoisomerization of azobenzene-based (Azo) molecules was observed in nanoscopic metal-molecule-metal junctions. The junctions were formed by using a conducting atomic force microscope (C-AFM) approach, where a metallic AFM tip was used to electrically contact a gold-supported Azo self-assembled monolayer. The measured 30-fold increase in conductance is consistent with the expected decrease in tunneling barrier length resulting from the conformational change of the Azo molecule.

One-to-one quantum dot-labeled single long DNA probes.

PubMed

He, Shibin; Huang, Bi-Hai; Tan, Junjun; Luo, Qing-Ying; Lin, Yi; Li, Jun; Hu, Yong; Zhang, Lu; Yan, Shihan; Zhang, Qi; Pang, Dai-Wen; Li, Lijia

2011-08-01

Quantum dots (QDs) have been received most attention due to their unique properties. Constructing QDs conjugated with certain number of biomolecules is considered as one of the most important research goals in nanobiotechnology. In this study, we report polymerase chain reaction (PCR) amplification of primer oligonucleotides bound to QDs, termed as QD-based PCR. Characterization of QD-based PCR products by gel electrophoresis and atomic force microscopy showed that QD-labeled long DNA strands were synthesized and only a single long DNA strand was conjugated with a QD. The QD-based PCR products still kept fluorescence properties. Moreover, the one-to-one QD-labeled long DNA conjugates as probes could detect a single-copy gene on maize chromosomes by fluorescence in situ hybridization. Labeling a single QD to a single long DNA will make detection of small single-copy DNA fragments, quantitative detection and single molecule imaging come true by nanotechnology, and it will promote medical diagnosis and basic biological research as well as nano-material fabrication. Copyright © 2011 Elsevier Ltd. All rights reserved.

Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

PubMed

Shen, Lin; Hu, Hao

2014-06-10

We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

Catalytic Enantioselective Synthesis of Quaternary Carbon Stereocenters

PubMed Central

Quasdorf, Kyle W.; Overman, Larry E.

2015-01-01

Preface Quaternary carbon stereocenters–carbon atoms to which four distinct carbon substituents are attached–are common features of molecules found in nature. However, prior to recent advances in chemical catalysis, there were few methods available for constructing single stereoisomers of this important structural motif. Here we discuss the many catalytic enantioselective reactions developed during the past decade for synthesizing organic molecules containing such carbon atoms. This progress now makes it possible to selectively incorporate quaternary stereocenters in many high-value organic molecules for use in medicine, agriculture, and other areas. PMID:25503231

Effects of quantum coherence and interference in atoms near nanoparticles

NASA Astrophysics Data System (ADS)

Dhayal, Suman; Rostovtsev, Yuri V.

2016-04-01

Optical properties of ensembles of realistic quantum emitters coupled to plasmonic systems are studied by using adequate models that can take into account full atomic geometry. In particular, the coherent effects such as forming "dark states," optical pumping, coherent Raman scattering, and the stimulated Raman adiabatic passage (STIRAP) are revisited in the presence of metallic nanoparticles. It is shown that the dark states are still formed but they have more complicated structure, and the optical pumping and the STIRAP cannot be employed in the vicinity of plasmonic nanostructures. Also, there is a huge difference in the behavior of the local atomic polarization and the atomic polarization averaged over an ensemble of atoms homogeneously spread near nanoparticles. The average polarization is strictly related to the polarization induced by the external field, while the local polarization can be very different from the one induced by the external field. This is important for the excitation of single molecules, e.g., different components of scattering from single molecules can be used for their efficient detection.

Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model

NASA Astrophysics Data System (ADS)

Li, Chunhua; Lv, Dashuai; Zhang, Lei; Yang, Feng; Wang, Cunxin; Su, Jiguo; Zhang, Yang

2016-07-01

Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regions between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.

Composition and conductance distributions of single GeSi quantum rings studied by conductive atomic force microscopy combined with selective chemical etching.

PubMed

Lv, Y; Cui, J; Jiang, Z M; Yang, X J

2013-02-15

Atomic force microscopy imaging combined with selective chemical etching is employed to quantitatively investigate three-dimensional (3D) composition distributions of single GeSi quantum rings (QRs). In addition, the 3D quantitative composition distributions and the corresponding conductance distributions are simultaneously obtained on the same single GeSi QRs by conductive atomic force microscopy combined with selective chemical etching, allowing us to investigate the correlations between the conductance and composition distributions of single QRs. The results show that the QRs' central holes have higher Ge content, but exhibit lower conductance, indicating that the QRs' conductance distribution is not consistent with their composition distribution. By comparing the topography, composition and conductance profiles of the same single QRs before and after different etching processes, it is found that the conductance distributions of GeSi QRs do not vary with the change of composition distribution. Instead, the QRs' conductance distributions are found to be consistent with their topographic shapes, which can be supposed to be due to the shape determined electronic structures.

A quantum spin-probe molecular microscope

NASA Astrophysics Data System (ADS)

Perunicic, V. S.; Hill, C. D.; Hall, L. T.; Hollenberg, L. C. L.

2016-10-01

Imaging the atomic structure of a single biomolecule is an important challenge in the physical biosciences. Whilst existing techniques all rely on averaging over large ensembles of molecules, the single-molecule realm remains unsolved. Here we present a protocol for 3D magnetic resonance imaging of a single molecule using a quantum spin probe acting simultaneously as the magnetic resonance sensor and source of magnetic field gradient. Signals corresponding to specific regions of the molecule's nuclear spin density are encoded on the quantum state of the probe, which is used to produce a 3D image of the molecular structure. Quantum simulations of the protocol applied to the rapamycin molecule (C51H79NO13) show that the hydrogen and carbon substructure can be imaged at the angstrom level using current spin-probe technology. With prospects for scaling to large molecules and/or fast dynamic conformation mapping using spin labels, this method provides a realistic pathway for single-molecule microscopy.

A single molecule assay to probe monovalent and multivalent bonds between hyaluronan and its key leukocyte receptor CD44 under force

NASA Astrophysics Data System (ADS)

Bano, Fouzia; Banerji, Suneale; Howarth, Mark; Jackson, David G.; Richter, Ralf P.

2016-09-01

Glycosaminoglycans (GAGs), a category of linear, anionic polysaccharides, are ubiquitous in the extracellular space, and important extrinsic regulators of cell function. Despite the recognized significance of mechanical stimuli in cellular communication, however, only few single molecule methods are currently available to study how monovalent and multivalent GAG·protein bonds respond to directed mechanical forces. Here, we have devised such a method, by combining purpose-designed surfaces that afford immobilization of GAGs and receptors at controlled nanoscale organizations with single molecule force spectroscopy (SMFS). We apply the method to study the interaction of the GAG polymer hyaluronan (HA) with CD44, its receptor in vascular endothelium. Individual bonds between HA and CD44 are remarkably resistant to rupture under force in comparison to their low binding affinity. Multiple bonds along a single HA chain rupture sequentially and independently under load. We also demonstrate how strong non-covalent bonds, which are versatile for controlled protein and GAG immobilization, can be effectively used as molecular anchors in SMFS. We thus establish a versatile method for analyzing the nanomechanics of GAG·protein interactions at the level of single GAG chains, which provides new molecular-level insight into the role of mechanical forces in the assembly and function of GAG-rich extracellular matrices.

Calculating constants of the rates of the reactions of excitation, ionization, and atomic exchange: A model of a shock oscillator with a change of the Hamiltonian of the system

NASA Astrophysics Data System (ADS)

Tsyganov, D. L.

2017-11-01

A new model for calculating the rates of reactions of excitation, ionization, and atomic exchange is proposed. Diatomic molecule AB is an unstructured particle M upon the exchange of elastic-vibrational (VT) energy, i.e., a model of a shock forceful oscillator with a change in Hamiltonian (SFOH). The SFOH model is based on the quantum theory of strong perturbations. The SFOH model allows generalization in simulating the rates of the reactions of excitation, ionization, and atomic exchange in the vibrational-vibrational (VV) energy exchange of diatomic molecules, and the exchange of VV- and VT-energy of polyatomic molecules. The rate constants of the excitation of metastables A 3Σ u +, B 3Π g , W 3Δ u , B'3Σ u -, a'3Σ u -, and the ionization of a nitrogen molecules from ground state X2Σ g + upon a collision with a heavy structureless particle (a nitrogen molecule), are found as examples.

Optically stimulated slowing of polar heavy-atom molecules with a constant beat phase

NASA Astrophysics Data System (ADS)

Yin, Yanning; Xu, Supeng; Xia, Meng; Xia, Yong; Yin, Jianping

2018-04-01

Polar heavy-atom molecules have been well recognized as promising candidates for precision measurements and tests of fundamental physics. A much slower molecular beam to increase the interaction time should lead to a more sensitive measurement. Here we theoretically demonstrate the possibility of the stimulated longitudinal slowing of heavy-atom molecules by the coherent optical bichromatic force with a constant beat phase. Taking the YbF meolecule as an example, we show that a rapid and short-distance deceleration of heavy molecules by a phase-compensation method is feasible with moderate conditions. A molecular beam of YbF with a forward velocity of 120 m/s can be decelerated below 10 m/s within a distance of 3.5 cm and with a laser irradiance for each traveling wave of 107.2 W/cm 2 . Our proposed slowing method could be a promising approach to break through the space constraint or the limited capture efficiency of molecules loadable into a magneto-optical trap in traditional deceleration schemes, opening the possibility for a significant improvement of the precision measurement sensitivity.

Quantitative analysis of single-molecule force spectroscopy on folded chromatin fibers

PubMed Central

Meng, He; Andresen, Kurt; van Noort, John

2015-01-01

Single-molecule techniques allow for picoNewton manipulation and nanometer accuracy measurements of single chromatin fibers. However, the complexity of the data, the heterogeneity of the composition of individual fibers and the relatively large fluctuations in extension of the fibers complicate a structural interpretation of such force-extension curves. Here we introduce a statistical mechanics model that quantitatively describes the extension of individual fibers in response to force on a per nucleosome basis. Four nucleosome conformations can be distinguished when pulling a chromatin fiber apart. A novel, transient conformation is introduced that coexists with single wrapped nucleosomes between 3 and 7 pN. Comparison of force-extension curves between single nucleosomes and chromatin fibers shows that embedding nucleosomes in a fiber stabilizes the nucleosome by 10 kBT. Chromatin fibers with 20- and 50-bp linker DNA follow a different unfolding pathway. These results have implications for accessibility of DNA in fully folded and partially unwrapped chromatin fibers and are vital for understanding force unfolding experiments on nucleosome arrays. PMID:25779043

Synthesis, XRD single crystal structure analysis, vibrational spectral analysis, molecular dynamics and molecular docking studies of 2-(3-methoxy-4-hydroxyphenyl) benzothiazole

NASA Astrophysics Data System (ADS)

Sarau Devi, A.; Aswathy, V. V.; Sheena Mary, Y.; Yohannan Panicker, C.; Armaković, Stevan; Armaković, Sanja J.; Ravindran, Reena; Van Alsenoy, C.

2017-11-01

The vibrational spectra and corresponding vibrational assignments of 2-(3-methoxy-4-hydroxyphenyl)benzothiazole is reported. Single crystal XRD data of the title compound is reported and the orientation of methoxy group is cis to nitrogen atom of the thiazole ring. The phenyl ring breathing modes of the title compound are assigned at 1042 and 731 cm-1 theoretically. The charge transfer within the molecule is studied using frontier molecular orbital analysis. The chemical reactivity descriptors are calculated theoretically. The NMR spectral data predicted theoretically are in good agreement with the experimental data. The strong negative region spread over the phenyl rings, nitrogen atom and oxygen atom of the hydroxyl group in the MEP plot is due to the immense conjugative and hyper conjugative resonance charge delocalization of π-electrons. Molecule sites prone to electrophilic attacks have been determined by analysis of ALIE surfaces, while Fukui functions provided further insight into the local reactivity properties of title molecule. Autoxidation properties have been investigated by calculation of bond dissociation energies (BDEs) of hydrogen abstraction, while BDEs of the rest of the single acyclic bonds were valuable for the further investigation of degradation properties. Calculation of radial distribution functions was performed in order to determine which atoms of the title molecule have pronounced interactions with water molecules. The title compound forms a stable complex with aryl hydrocarbon receptor and can be a lead compound for developing new anti-tumor drug. Antimicrobial properties of the title compound was screened against one bacterial culture Escherchia coli and four fungal cultures viz., Aspergillus niger, Pencillum chrysogenum, Saccharomyces cerevisiae and Rhyzopus stolonifer.

Potentials of mean force for biomolecular simulations: Theory and test on alanine dipeptide

NASA Astrophysics Data System (ADS)

Pellegrini, Matteo; Grønbech-Jensen, Niels; Doniach, Sebastian

1996-06-01

We describe a technique for generating potentials of mean force (PMF) between solutes in an aqueous solution. We first generate solute-solvent correlation functions (CF) using Monte Carlo (MC) simulations in which we place a single atom solute in a periodic boundary box containing a few hundred water molecules. We then make use of the Kirkwood superposition approximation, where the 3-body correlation function is approximated as the product of 2-body CFs, to describe the mean water density around two solutes. Computing the force generated on the solutes by this average water density allows us to compute potentials of mean force between the two solutes. For charged solutes an additional approximation involving dielectric screening is made, by setting the dielectric constant of water to ɛ=80. These potentials account, in an approximate manner, for the average effect of water on the atoms. Following the work of Pettitt and Karplus [Chem. Phys. Lett. 121, 194 (1985)], we approximate the n-body potential of mean force as a sum of the pairwise potentials of mean force. This allows us to run simulations of biomolecules without introducing explicit water, hence gaining several orders of magnitude in efficiency with respect to standard molecular dynamics techniques. We demonstrate the validity of this technique by first comparing the PMFs for methane-methane and sodium-chloride generated with this procedure, with those calculated with a standard Monte Carlo simulation with explicit water. We then compare the results of the free energy profiles between the equilibria of alanine dipeptide generated by the two methods.

Single Molecule Measurements of Interaction Free Energies Between the Proteins Within Binary and Ternary SNARE Complexes

PubMed Central

Liu, W.; Montana, Vedrana; Parpura, Vladimir; Mohideen, U.

2010-01-01

We use an Atomic Force Microscope based single molecule measurements to evaluate the activation free energy in the interaction of SNARE proteins syntaxin 1A, SNAP25B and synaptobrevin 2 which regulate intracellular fusion of vesicles with target membranes. The dissociation rate of the binary syntaxin-synaptobrevin and the ternary syntaxin-SNAP25B-synaptobrevin complex was measured from the rupture force distribution as a function of the rate of applied force. The temperature dependence of the spontaneous dissociation rate was used to obtain the activation energy to the transition state of 19.8 ± 3.5 kcal/mol = 33 ± 6 kBT and 25.7 ± 3.0 kcal/mol = 43 ± 5 kBT for the binary and ternary complex, respectively. They are consistent with those measured previously for the ternary complex in lipid membranes and are of order expected for bilayer fusion and pore formation. The ΔG was 12.4–16.6 kcal/mol = 21–28 kBT and 13.8–18.0 kcal/mol = 23–30 kBT for the binary and ternary complex, respectively. The ternary complex was more stable by 1.4 kcal/mol = 2.3 kBT, consistent with the spontaneous dissociation rates. The higher adhesion energies and smaller molecular extensions measured with SNAP25B point to its possible unique and important physiological role in tethering/docking the vesicle in closer proximity to the plasma membrane and increasing the probability for fusion completion. PMID:20107522

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

PubMed

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

2017-09-01

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

Solvent-driven reductive activation of carbon dioxide by gold anions.

PubMed

Knurr, Benjamin J; Weber, J Mathias

2012-11-14

Catalytic activation and electrochemical reduction of CO(2) for the formation of chemically usable feedstock and fuel are central goals for establishing a carbon neutral fuel cycle. The role of solvent molecules in catalytic processes is little understood, although solvent-solute interactions can strongly influence activated intermediate species. We use vibrational spectroscopy of mass-selected Au(CO(2))(n)(-) cluster ions to probe the solvation of AuCO(2)(-) as a model for a reactive intermediate in the reductive activation of a CO(2) ligand by a single-atom catalyst. For the first few solvent molecules, solvation of the complex preferentially occurs at the CO(2) moiety, enhancing reductive activation through polarization of the excess charge onto the partially reduced ligand. At higher levels of solvation, direct interaction of additional solvent molecules with the Au atom diminishes reduction. The results show how the solvation environment can enhance or diminish the effects of a catalyst, offering design criteria for single-atom catalyst engineering.

Correlation between surface morphology and surface forces of protein A adsorbed on mica.

PubMed Central

Ohnishi, S; Murata, M; Hato, M

1998-01-01

We have investigated the morphology and surface forces of protein A adsorbed on mica surface in the protein solutions of various concentrations. The force-distance curves, measured with a surface force apparatus (SFA), were interpreted in terms of two different regimens: a "large-distance" regimen in which an electrostatic double-layer force dominates, and an "adsorbed layer" regimen in which a force of steric origin dominates. To further clarify the forces of steric origin, the surface morphology of the adsorbed protein layer was investigated with an atomic force microscope (AFM) because the steric repulsive forces are strongly affected by the adsorption mode of protein A molecules on mica. At lower protein concentrations (2 ppm, 10 ppm), protein A molecules were adsorbed "side-on" parallel to the mica surfaces, forming a monolayer of approximately 2.5 nm. AFM images at higher concentrations (30 ppm, 100 ppm) showed protruding structures over the monolayer, which revealed that the adsorbed protein A molecules had one end oriented into the solution, with the remainder of each molecule adsorbed side-on to the mica surface. These extending ends of protein A overlapped each other and formed a "quasi-double layer" over the mica surface. These AFM images proved the existence of a monolayer of protein A molecules at low concentrations and a "quasi-double layer" with occasional protrusions at high concentrations, which were consistent with the adsorption mode observed in the force-distance curves. PMID:9449346

Optimizing atomic force microscopy for characterization of diamond-protein interfaces

NASA Astrophysics Data System (ADS)

Rezek, Bohuslav; Ukraintsev, Egor; Kromka, Alexander

2011-12-01

Atomic force microscopy (AFM) in contact mode and tapping mode is employed for high resolution studies of soft organic molecules (fetal bovine serum proteins) on hard inorganic diamond substrates in solution and air. Various effects in morphology and phase measurements related to the cantilever spring constant, amplitude of tip oscillations, surface approach, tip shape and condition are demonstrated and discussed based on the proposed schematic models. We show that both diamond and proteins can be mechanically modified by Si AFM cantilever. We propose how to choose suitable cantilever type, optimize scanning parameters, recognize and minimize various artifacts, and obtain reliable AFM data both in solution and in air to reveal microscopic characteristics of protein-diamond interfaces. We also suggest that monocrystalline diamond is well defined substrate that can be applicable for fundamental studies of molecules on surfaces in general.

Coupling density functional theory to polarizable force fields for efficient and accurate Hamiltonian molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Schwörer, Magnus; Breitenfeld, Benedikt; Tröster, Philipp; Bauer, Sebastian; Lorenzen, Konstantin; Tavan, Paul; Mathias, Gerald

2013-06-01

Hybrid molecular dynamics (MD) simulations, in which the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 103-105 molecules, pose a challenge. A corresponding computational approach should guarantee energy conservation, exclude artificial distortions of the electron density at the interface between the DFT and PMM fragments, and should treat the long-range electrostatic interactions within the hybrid simulation system in a linearly scaling fashion. Here we describe a corresponding Hamiltonian DFT/(P)MM implementation, which accounts for inducible atomic dipoles of a PMM environment in a joint DFT/PMM self-consistency iteration. The long-range parts of the electrostatics are treated by hierarchically nested fast multipole expansions up to a maximum distance dictated by the minimum image convention of toroidal boundary conditions and, beyond that distance, by a reaction field approach such that the computation scales linearly with the number of PMM atoms. Short-range over-polarization artifacts are excluded by using Gaussian inducible dipoles throughout the system and Gaussian partial charges in the PMM region close to the DFT fragment. The Hamiltonian character, the stability, and efficiency of the implementation are investigated by hybrid DFT/PMM-MD simulations treating one molecule of the water dimer and of bulk water by DFT and the respective remainder by PMM.

Torque measurement at the single-molecule level.

PubMed

Forth, Scott; Sheinin, Maxim Y; Inman, James; Wang, Michelle D

2013-01-01

Methods for exerting and measuring forces on single molecules have revolutionized the study of the physics of biology. However, it is often the case that biological processes involve rotation or torque generation, and these parameters have been more difficult to access experimentally. Recent advances in the single-molecule field have led to the development of techniques that add the capability of torque measurement. By combining force, displacement, torque, and rotational data, a more comprehensive description of the mechanics of a biomolecule can be achieved. In this review, we highlight a number of biological processes for which torque plays a key mechanical role. We describe the various techniques that have been developed to directly probe the torque experienced by a single molecule, and detail a variety of measurements made to date using these new technologies. We conclude by discussing a number of open questions and propose systems of study that would be well suited for analysis with torsional measurement techniques.

Recognition Imaging with a DNA Aptamer

PubMed Central

Lin, Liyun; Wang, Hongda; Liu, Yan; Yan, Hao; Lindsay, Stuart

2006-01-01

We have used a DNA-aptamer tethered to an atomic force microscope probe to carry out recognition imaging of IgE molecules attached to a mica substrate. The recognition was efficient (∼90%) and specific, being blocked by injection of IgE molecules in solution, and not being interfered with by high concentrations of a second protein. The signal/noise ratio of the recognition signal was better than that obtained with antibodies, despite the fact that the average force required to break the aptamer-protein bonds was somewhat smaller. PMID:16513776

Probing microbubble targeting with atomic force microscopy.

PubMed

Sboros, V; Glynos, E; Ross, J A; Moran, C M; Pye, S D; Butler, M; McDicken, W N; Brown, S B; Koutsos, V

2010-10-01

Microbubble science is expanding beyond ultrasound imaging applications to biological targeting and drug/gene delivery. The characteristics of molecular targeting should be tested by a measurement system that can assess targeting efficacy and strength. Atomic force microscopy (AFM) is capable of piconewton force resolution, and is reported to measure the strength of single hydrogen bonds. An in-house targeted microbubble modified using the biotin-avidin chemistry and the CD31 antibody was used to probe cultures of Sk-Hep1 hepatic endothelial cells. We report that the targeted microbubbles provide a single distribution of adhesion forces with a median of 93pN. This interaction is assigned to the CD31 antibody-antigen unbinding event. Information on the distances between the interaction forces was obtained and could be important for future microbubble fabrication. In conclusion, the capability of single microbubbles to target cell lines was shown to be feasible with AFM.

Mechanical Stability of a High-Affinity Toxin Anchor from the Pathogen Clostridium perfringens.

PubMed

Milles, Lukas F; Bayer, Edward A; Nash, Michael A; Gaub, Hermann E

2017-04-20

The opportunistic pathogen Clostridium perfringens assembles its toxins and carbohydrate-active enzymes by the high-affinity cohesin-dockerin (Coh-Doc) interaction. Coh-Doc interactions characterized previously have shown considerable resilience toward mechanical stress. Here, we aimed to determine the mechanics of this interaction from C. perfringens in the context of a pathogen. Using atomic force microscopy based single-molecule force spectroscopy (AFM-SMFS) we probed the mechanical properties of the interaction of a dockerin from the μ-toxin with the GH84C X82 cohesin domain of C. perfringens. Most probable complex rupture forces were found to be approximately 60 pN and an estimate of the binding potential width was performed. The dockerin was expressed with its adjacent FIVAR (found in various architectures) domain, whose mechanostability we determined to be very similar to the complex. Additionally, fast refolding of this domain was observed. The Coh-Doc interaction from C. perfringens is the mechanically weakest observed to date. Our results establish the relevant force range of toxin assembly mechanics in pathogenic Clostridia.

Graphene Visualizes the Ion Distribution on Air-Cleaved Mica.

PubMed

Bampoulis, Pantelis; Sotthewes, Kai; Siekman, Martin H; Zandvliet, Harold J W; Poelsema, Bene

2017-03-06

The distribution of potassium (K + ) ions on air-cleaved mica is important in many interfacial phenomena such as crystal growth, self-assembly and charge transfer on mica. However, due to experimental limitations to nondestructively probe single ions and ionic domains, their exact lateral organization is yet unknown. We show, by the use of graphene as an ultra-thin protective coating and scanning probe microscopies, that single potassium ions form ordered structures that are covered by an ice layer. The K + ions prefer to minimize the number of nearest neighbour K + ions by forming row-like structures as well as small domains. This trend is a result of repulsive ionic forces between adjacent ions, weakened due to screening by the surrounding water molecules. Using high resolution conductive atomic force microscopy maps, the local conductance of the graphene is measured, revealing a direct correlation between the K + distribution and the structure of the ice layer. Our results shed light on the local distribution of ions on the air-cleaved mica, solving a long-standing enigma. They also provide a detailed understanding of charge transfer from the ionic domains towards graphene.

Mystery of the Hidden Cosmos [Complex Dark Matter

DOE PAGES

Dobrescu, Bogdan A.; Lincoln, Don

2015-06-16

Scientists know there must be more matter in the universe than what is visible. Searches for this dark matter have focused on a single unseen particle, but decades of experiments have been unsuccessful at finding it. Exotic possibilities for dark matter are looking increasingly plausible. Rather than just one particle, dark matter could contain an entire world of particles and forces that barely interact with normal matter. Complex dark matter could form dark atoms and molecules and even clump together to make hidden galactic disks that overlap with the spiral arms of the Milky Way and other galaxies. Experiments aremore » under way to search for evidence of such a dark sector.« less

Machine learning of accurate energy-conserving molecular force fields.

PubMed

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

2017-05-01

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

Machine learning of accurate energy-conserving molecular force fields

PubMed Central

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

2017-01-01

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

Characterization of fiber-forming peptides and proteins by means of atomic force microscopy.

PubMed

Creasey, Rhiannon G; Gibson, Christopher T; Voelcker, Nicolas H

2012-05-01

The atomic force microscope (AFM) is widely used in biological sciences due to its ability to perform imaging experiments at high resolution in a physiological environment, without special sample preparation such as fixation or staining. AFM is unique, in that it allows single molecule information of mechanical properties and molecular recognition to be gathered. This review sets out to identify methodological applications of AFM for characterization of fiber-forming proteins and peptides. The basics of AFM operation are detailed, with in-depth information for any life scientist to get a grasp on AFM capabilities. It also briefly describes antibody recognition imaging and mapping of nanomechanical properties on biological samples. Subsequently, examples of AFM application to fiber-forming natural proteins, and fiber-forming synthetic peptides are given. Here, AFM is used primarily for structural characterization of fibers in combination with other techniques, such as circular dichroism and fluorescence spectroscopy. More recent developments in antibody recognition imaging to identify constituents of protein fibers formed in human disease are explored. This review, as a whole, seeks to encourage the life scientists dealing with protein aggregation phenomena to consider AFM as a part of their research toolkit, by highlighting the manifold capabilities of this technique.

The accuracy of ab initio calculations without ab initio calculations for charged systems: Kriging predictions of atomistic properties for ions in aqueous solutions

NASA Astrophysics Data System (ADS)

Di Pasquale, Nicodemo; Davie, Stuart J.; Popelier, Paul L. A.

2018-06-01

Using the machine learning method kriging, we predict the energies of atoms in ion-water clusters, consisting of either Cl- or Na+ surrounded by a number of water molecules (i.e., without Na+Cl- interaction). These atomic energies are calculated following the topological energy partitioning method called Interacting Quantum Atoms (IQAs). Kriging predicts atomic properties (in this case IQA energies) by a model that has been trained over a small set of geometries with known property values. The results presented here are part of the development of an advanced type of force field, called FFLUX, which offers quantum mechanical information to molecular dynamics simulations without the limiting computational cost of ab initio calculations. The results reported for the prediction of the IQA components of the energy in the test set exhibit an accuracy of a few kJ/mol, corresponding to an average error of less than 5%, even when a large cluster of water molecules surrounding an ion is considered. Ions represent an important chemical system and this work shows that they can be correctly taken into account in the framework of the FFLUX force field.

Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii

PubMed Central

2012-01-01

Background The Poisson-Boltzmann (PB) equation and its linear approximation have been widely used to describe biomolecular electrostatics. Generalized Born (GB) models offer a convenient computational approximation for the more fundamental approach based on the Poisson-Boltzmann equation, and allows estimation of pairwise contributions to electrostatic effects in the molecular context. Results We have implemented in a single program most common analyses of the electrostatic properties of proteins. The program first computes generalized Born radii, via a surface integral and then it uses generalized Born radii (using a finite radius test particle) to perform electrostic analyses. In particular the ouput of the program entails, depending on user's requirement: 1) the generalized Born radius of each atom; 2) the electrostatic solvation free energy; 3) the electrostatic forces on each atom (currently in a dvelopmental stage); 4) the pH-dependent properties (total charge and pH-dependent free energy of folding in the pH range -2 to 18; 5) the pKa of all ionizable groups; 6) the electrostatic potential at the surface of the molecule; 7) the electrostatic potential in a volume surrounding the molecule; Conclusions Although at the expense of limited flexibility the program provides most common analyses with requirement of a single input file in PQR format. The results obtained are comparable to those obtained using state-of-the-art Poisson-Boltzmann solvers. A Linux executable with example input and output files is provided as supplementary material. PMID:22536964

A Simple Bioconjugate Attachment Protocol for Use in Single Molecule Force Spectroscopy Experiments Based on Mixed Self-Assembled Monolayers

PubMed Central

Attwood, Simon J.; Simpson, Anna M. C.; Stone, Rachael; Hamaia, SamirW.; Roy, Debdulal; Farndale, RichardW.; Ouberai, Myriam; Welland, Mark E.

2012-01-01

Single molecule force spectroscopy is a technique that can be used to probe the interaction force between individual biomolecular species. We focus our attention on the tip and sample coupling chemistry, which is crucial to these experiments. We utilised a novel approach of mixed self-assembled monolayers of alkanethiols in conjunction with a heterobifunctional crosslinker. The effectiveness of the protocol is demonstrated by probing the biotin-avidin interaction. We measured unbinding forces comparable to previously reported values measured at similar loading rates. Specificity tests also demonstrated a significant decrease in recognition after blocking with free avidin. PMID:23202965

Synthesis and crystal structure of the coordination compound of pyridoxine with manganese sulfate

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

Furmanova, N. G., E-mail: furm@ns.crys.ras.ru; Verin, I. A.; Shyityeva, N.

2011-11-15

The reaction of pyridoxine with manganese sulfate in an aqueous solution gave the coordination compound MnSO{sub 4} {center_dot} 2C{sub 8}H{sub 11}O{sub 3}N {center_dot} 2H{sub 2}O (I). The structure of I was determined from single-crystal X-ray diffraction data. In the centrosymmetric complex (sp. gr. P1-bar, Z = 1), the Mn atom is coordinated by two pyridoxine molecules and two water molecules, thus adopting an octahedral coordination. The sulfate anion is also at a center of symmetry and, consequently, is disordered. The pyridoxine molecules are coordinated to the metal atom through the oxygen atoms of the deprotonated hydroxyl group and the CH{submore » 2}OH group that retains the hydrogen atom. The nitrogen atom is protonated in such a way that the heterocycle assumes a pyridinium character. The crystal structure also contains six water molecules of crystallization. A thermogravimetric study showed that the decomposition of I occurs in several successive steps, such as dehydration, the combustion of organic ligands, and the formation of an inorganic residue.« less

Integrated magnetic tweezers and single-molecule FRET for investigating the mechanical properties of nucleic acid.

PubMed

Long, Xi; Parks, Joseph W; Stone, Michael D

2016-08-01

Many enzymes promote structural changes in their nucleic acid substrates via application of piconewton forces over nanometer length scales. Magnetic tweezers (MT) is a single molecule force spectroscopy method widely used for studying the energetics of such mechanical processes. MT permits stable application of a wide range of forces and torques over long time scales with nanometer spatial resolution. However, in any force spectroscopy experiment, the ability to monitor structural changes in nucleic acids with nanometer sensitivity requires the system of interest to be held under high degrees of tension to improve signal to noise. This limitation prohibits measurement of structural changes within nucleic acids under physiologically relevant conditions of low stretching forces. To overcome this challenge, researchers have integrated a spatially sensitive fluorescence spectroscopy method, single molecule-FRET, with MT to allow simultaneous observation and manipulation of nanoscale structural transitions over a wide range of forces. Here, we describe a method for using this hybrid instrument to analyze the mechanical properties of nucleic acids. We expect that this method for analysis of nucleic acid structure will be easily adapted for experiments aiming to interrogate the mechanical responses of other biological macromolecules. Copyright © 2016 Elsevier Inc. All rights reserved.

Integrated magnetic tweezers and single-molecule FRET for investigating the mechanical properties of nucleic acid

PubMed Central

Long, Xi; Parks, Joseph W.; Stone, Michael D.

2017-01-01

Many enzymes promote structural changes in their nucleic acid substrates via application of piconewton forces over nanometer length scales. Magnetic tweezers (MT) is a single molecule force spectroscopy method widely used for studying the energetics of such mechanical processes. MT permits stable application of a wide range of forces and torques over long time scales with nanometer spatial resolution. However, in any force spectroscopy experiment, the ability to monitor structural changes in nucleic acids with nanometer sensitivity requires the system of interest to be held under high degrees of tension to improve signal to noise. This limitation prohibits measurement of structural changes within nucleic acids under physiologically relevant conditions of low stretching forces. To overcome this challenge, researchers have integrated a spatially sensitive fluorescence spectroscopy method, single molecule-FRET, with MT to allow simultaneous observation and manipulation of nanoscale structural transitions over a wide range of forces. Here, we describe a method for using this hybrid instrument to analyze the mechanical properties of nucleic acids. We expect that this method for analysis of nucleic acid structure will be easily adapted for experiments aiming to interrogate the mechanical responses of other biological macromolecules. PMID:27320203

An important rule for realizing metal → half-metal → semiconductor transition in single-molecule junctions

NASA Astrophysics Data System (ADS)

Zeng, Jing; Chen, Ke-Qiu; Long, Mengqiu

2017-06-01

Recently, Zhong et al (2015 Nano Lett. 15 8091) found that two additional hydrogen atoms can be adsorbed to the opposite aza-bridging nitrogen atoms of the manganese phthalocyanine (MnPc) macrocycle when exposed to H2. Thus the symmetry of the MnPc molecule is changed from 4-fold to 2-fold. Motivated by this recent experiment, we theoretically investigate a MnPc-based single-molecule junction in this work and propose a simple and reliable way to realize the transition of its electronic properties. On the basis of spin-polarized density-functional theory calculations combined with the Keldysh nonequilibrium Green’s technique, we find that the gradual hydrogenation in MnPc molecules gives rise to the changes of the hardness of the electron density and spin-selective orbital decoupling, which eventually leads to the realization of the first ever metal  →  half-metal  →  semiconductor transition behavior in single-molecule junctions. Analysis of molecular projected self-consistent Hamiltonian, Mulliken population, and local density of states also reveals an important rule for realizing this transition behavior. Our research confirms that the hydrogenation of MnPc molecules can realize various molecular functionalities in unitary material background.

Toggling Bistable Atoms via Mechanical Switching of Bond Angle

NASA Astrophysics Data System (ADS)

Sweetman, Adam; Jarvis, Sam; Danza, Rosanna; Bamidele, Joseph; Gangopadhyay, Subhashis; Shaw, Gordon A.; Kantorovich, Lev; Moriarty, Philip

2011-04-01

We reversibly switch the state of a bistable atom by direct mechanical manipulation of bond angle using a dynamic force microscope. Individual buckled dimers at the Si(100) surface are flipped via the formation of a single covalent bond, actuating the smallest conceivable in-plane toggle switch (two atoms) via chemical force alone. The response of a given dimer to a flip event depends critically on both the local and nonlocal environment of the target atom—an important consideration for future atomic scale fabrication strategies.

Molecular mechanisms of mechanotransduction in integrin-mediated cell-matrix adhesion

PubMed Central

Li, Zhenhai; Lee, Hyunjung; Zhu, Cheng

2016-01-01

Cell-matrix adhesion complexes are multi-protein structures linking the extracellular matrix (ECM) to the cytoskeleton. They are essential to both cell motility and function by bidirectionally sensing and transmitting mechanical and biochemical stimulations. Several types of cell-matrix adhesions have been identified and they share many key molecular components, such as integrins and actin-integrin linkers. Mechanochemical coupling between ECM molecules and the actin cytoskeleton has been observed from the single cell to the single molecule level and from immune cells to neuronal cells. However, the mechanisms underlying force regulation of integrin-mediated mechanotransduction still need to be elucidated. In this review article, we focus on integrin-mediated adhesions and discuss force regulation of cell-matrix adhesions and key adaptor molecules, three different force-dependent behaviors, and molecular mechanisms for mechanochemical coupling in force regulation. PMID:27720950

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

NASA Technical Reports Server (NTRS)

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

1986-01-01

The physical forces between atoms and molecules are important in a number of processes of practical importance, including line broadening in radiative processes, gas and crystal properties, adhesion, and thin films. The components of the physical forces between noble gas atoms, alkali ions, and halogen ions are analyzed and a data base for the dispersion forces is developed from the literature based on evaluations with the harmonic oscillator dispersion model for higher order coefficients. The Zener model of the repulsive core is used in the context of the recent asymptotic wave functions of Handler and Smith; and an effective ionization potential within the Handler and Smith wave functions is defined to analyze the two body potential data of Waldman and Gordon, the alkali-halide molecular data, and the noble gas crystal and salt crystal data. A satisfactory global fit to this molecular and crystal data is then reproduced by the model to within several percent. Surface potentials are evaluated for noble gas atoms on noble gas and salt crystal surfaces with surface tension neglected. Within this context, the noble gas surface potentials on noble gas and salt crystals are considered to be accurate to within several percent.

Laser Cooling the Diatomic Molecule CaH

NASA Astrophysics Data System (ADS)

Velasquez, Joe, III; Di Rosa, Michael

2014-06-01

To laser-cool a species, a closed (or nearly closed) cycle is required to dissipate translational energy through many directed laser-photon absorption and subsequent randomly-directed spontaneous emission events. Many atoms lend themselves to such a closed-loop cooling cycle. Attaining laser-cooled molecular species is challenging because of their inherently complex internal structure, yet laser-cooling molecules could lead to studies in interesting chemical dynamics among other applications. Typically, laser-cooled atoms are assembled into molecules through photoassociation or Feschbach resonance. CaH is one of a few molecules whose internal structure is quite atom-like, allowing a nearly closed cycle without the need for many repumping lasers. We will also present our work-to-date on laser cooling this molecule. We employ traditional pulsed atomic/molecular beam techniques with a laser vaporization source to generate species with well-defined translational energies over a narrow range of velocity. In this way, we can apply laser-cooling to most species in the beam along a single dimension (the beam's axis). This project is funded by the LDRD program of the Los Alamos National Laboratory.

A Physical Model to Help Explain Evaporation

ERIC Educational Resources Information Center

Branca, M.; Soletta, I.

2014-01-01

One of the basic ideas when studying science is that matter is composed of particles (atoms or molecules) and these are in a constant state of agitation. In the solid or liquid state the molecules are attracted to each other, while in the gaseous state they have sufficient energy to overcome the forces of cohesion and can move away from one…

Inter-dot strain field effect on the optoelectronic properties of realistic InP lateral quantum-dot molecules

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

Barettin, Daniele, E-mail: Daniele.Barettin@uniroma2.it; Auf der Maur, Matthias; De Angelis, Roberta

2015-03-07

We report on numerical simulations of InP surface lateral quantum-dot molecules on In{sub 0.48}Ga{sub 0.52 }P buffer, using a model strictly derived by experimental results by extrapolation of the molecules shape from atomic force microscopy images. Our study has been inspired by the comparison of a photoluminescence spectrum of a high-density InP surface quantum dot sample with a numerical ensemble average given by a weighted sum of simulated single quantum-dot spectra. A lack of experimental optical response from the smaller dots of the sample is found to be due to strong inter-dot strain fields, which influence the optoelectronic properties of lateralmore » quantum-dot molecules. Continuum electromechanical, k{sup →}·p{sup →} bandstructure, and optical calculations are presented for two different molecules, the first composed of two dots of nearly identical dimensions (homonuclear), the second of two dots with rather different sizes (heteronuclear). We show that in the homonuclear molecule the hydrostatic strain raises a potential barrier for the electrons in the connection zone between the dots, while conversely the holes do not experience any barrier, which considerably increases the coupling. Results for the heteronuclear molecule show instead that its dots do not appear as two separate and distinguishable structures, but as a single large dot, and no optical emission is observed in the range of higher energies where the smaller dot is supposed to emit. We believe that in samples of such a high density the smaller dots result as practically incorporated into bigger molecular structures, an effect strongly enforced by the inter-dot strain fields, and consequently it is not possible to experimentally obtain a separate optical emission from the smaller dots.« less

Inter-dot strain field effect on the optoelectronic properties of realistic InP lateral quantum-dot molecules

NASA Astrophysics Data System (ADS)

Barettin, Daniele; Auf der Maur, Matthias; De Angelis, Roberta; Prosposito, Paolo; Casalboni, Mauro; Pecchia, Alessandro

2015-03-01

We report on numerical simulations of InP surface lateral quantum-dot molecules on In0.48Ga0.52P buffer, using a model strictly derived by experimental results by extrapolation of the molecules shape from atomic force microscopy images. Our study has been inspired by the comparison of a photoluminescence spectrum of a high-density InP surface quantum dot sample with a numerical ensemble average given by a weighted sum of simulated single quantum-dot spectra. A lack of experimental optical response from the smaller dots of the sample is found to be due to strong inter-dot strain fields, which influence the optoelectronic properties of lateral quantum-dot molecules. Continuum electromechanical, k →.p → bandstructure, and optical calculations are presented for two different molecules, the first composed of two dots of nearly identical dimensions (homonuclear), the second of two dots with rather different sizes (heteronuclear). We show that in the homonuclear molecule the hydrostatic strain raises a potential barrier for the electrons in the connection zone between the dots, while conversely the holes do not experience any barrier, which considerably increases the coupling. Results for the heteronuclear molecule show instead that its dots do not appear as two separate and distinguishable structures, but as a single large dot, and no optical emission is observed in the range of higher energies where the smaller dot is supposed to emit. We believe that in samples of such a high density the smaller dots result as practically incorporated into bigger molecular structures, an effect strongly enforced by the inter-dot strain fields, and consequently it is not possible to experimentally obtain a separate optical emission from the smaller dots.

An approach to spin-resolved molecular gas microscopy

NASA Astrophysics Data System (ADS)

Covey, Jacob P.; De Marco, Luigi; Acevedo, Óscar L.; Rey, Ana Maria; Ye, Jun

2018-04-01

Ultracold polar molecules are an ideal platform for studying many-body physics with long-range dipolar interactions. Experiments in this field have progressed enormously, and several groups are pursuing advanced apparatus for manipulation of molecules with electric fields as well as single-atom-resolved in situ detection. Such detection has become ubiquitous for atoms in optical lattices and tweezer arrays, but has yet to be demonstrated for ultracold polar molecules. Here we present a proposal for the implementation of site-resolved microscopy for polar molecules, and specifically discuss a technique for spin-resolved molecular detection. We use numerical simulation of spin dynamics of lattice-confined polar molecules to show how such a scheme would be of utility in a spin-diffusion experiment.

PREFACE: NC-AFM 2003: Proceedings of the 6th International Conference on Non-contact Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Reichling, Michael

2004-02-01

Direct nanoscale and atomic resolution imaging is a key issue in nanoscience and nanotechnology. The invention of the dynamic force microscope in the early 1990s was an important step forward in this direction as this instrument provides a universal tool for measuring the topography and many other physical and chemical properties of surfaces at the nanoscale. Operation in the so-called non-contact mode now allows direct atomic resolution imaging of electrically insulating surfaces and nanostructures which has been an unsolved problem during the first decade of nanotechnology. Today, we face a most rapid development of the technique and an extension of its capabilities far beyond imaging; atomically resolved force spectroscopy provides information about local binding properties and researchers now develop sophisticated schemes of force controlled atomic manipulation with the tip of the force microscope. Progress in the field of non-contact force microscopy is discussed at the annually held NC-AFM conferences that are part of a series started in 1998 with a meeting in Osaka, Japan. The 6th International Conference on Non-contact Atomic Force Microscopy took place in Dingle, Ireland, from 31 August to 3 September 2003 and this special issue is a compilation of the original publications of work presented at this meeting. The papers published here well reflect recent achievements, current trends and some of the challenging new directions in non-contact force microscopy that have been discussed during the most stimulating conference days in Dingle. Fundamental aspects of forces and dissipation relevant in imaging and spectroscopy have been covered by experimental and theoretical contributions yielding a more detailed understanding of tip--surface interaction in force microscopy. Novel and improved imaging and spectroscopy techniques have been introduced that either improve the performance of force microscopy or pave the way towards new functionalities and applications. With regard to studies on the specific systems investigated, there was a strong emphasis on oxides and ionics, as well as on organic systems. Following previous pioneering work in uncovering the atomic structure of insulating oxides with force microscopy, it was shown in the meeting that this important class of materials is now accessible for a quantitative atomic scale surface characterization. Single organic molecules and ordered organic layers are building blocks for functional nanostructures currently developed in many laboratories for applications in molecular electronics and sensor technologies. The Dingle conference impressively demonstrated that dynamic force microscopy is ready for its application as an analytical tool for these promising future nanotechnologies. The meeting was a great success scientifically and participants enjoyed the beauty of the conference site. I would like to thank all members of the international steering committee, the programme committee and the co-chairs, J Pethica, A Shluger and G Thornton, for their efforts in preparing the meeting. The members of the local organising committee, J Ballentine-Armstrong, G Cross, S Dunne, S Jarvis and Ö Özer, kept the meeting running smoothly and created a very pleasant atmosphere. The generous financial support from Science Foundation Ireland (SFI), is greatly appreciated; SFI is dramatically raising the profile of Irish science. I would also like to express my sincere gratitude to N Couzin and the journal team from Institute of Physics Publishing for their editorial management and perfect co-operation in the preparation of this special issue.

Resolving DNA-ligand intercalation in the entropic stretching regime

NASA Astrophysics Data System (ADS)

Almaqwashi, Ali A.

Single molecule studies of DNA intercalation are typically conducted by applying stretching forces to obtain force-dependent DNA elongation measurements. The zero-force properties of DNA intercalation are determined by equilibrium and kinetic force-analysis. However, the applied stretching forces that are above the entropic regime (>5 pN) prevent DNA-DNA contact which may eliminate competitive DNA-ligand interactions. In particular, it is noted that cationic mono-intercalators investigated by single molecule force spectroscopy are mostly found to intercalate DNA with single rate, while bulk studies reported additional slower rates. Here, a proposed framework quantifies DNA intercalation by cationic ligands in competition with relatively rapid kinetic DNA-ligand aggregation. At a constant applied force in the entropic stretching regime, the analysis illustrates that DNA intercalation would be measurably optimized only within a narrow range of low ligand concentrations. As DNA intercalators are considered for potential DNA-targeted therapeutics, this analysis provides insights in tuning ligand concertation to maximize therapeutics efficiency.

SLAC All Access: Atomic, Molecular and Optical Science Instrument

ScienceCinema

Bozek, John

2018-02-13

John Bozek, a staff scientist at SLAC's Linac Coherent Light Source (LCLS) X-ray laser who manages the LCLS Soft X-ray Department, takes us behind the scenes at the Atomic, Molecular and Optical Science (AMO) instrument, the first of six experimental stations now operating at LCLS. Samples used in AMO experiments include atoms, molecules, clusters, and nanoscale objects such as protein crystals or viruses. Science performed at AMO includes fundamental studies of light-matter interactions in the extreme X-ray intensity of the LCLS pules, time-resolved studies of increasingly charged states of atoms and molecules, X-ray diffraction imaging of nanocrystals, and single-shot imaging of a variety of objects.

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

DOE PAGES

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

2017-01-24

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

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

PubMed

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

2017-02-14

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

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

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

Huang, Jing; Mei, Ye; König, Gerhard

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

Formation of ultracold molecules induced by a high-power single-frequency fiber laser

NASA Astrophysics Data System (ADS)

Fernandes Passagem, Henry; Colín-Rodríguez, Ricardo; Ventura da Silva, Paulo Cesar; Bouloufa-Maafa, Nadia; Dulieu, Olivier; Marcassa, Luis Gustavo

2017-02-01

The influence of a high-power single-frequency fiber laser on the formation of ultracold 85Rb2 molecules is investigated as a function of its frequency (in the 1062-1070 nm range) in a magneto-optical trap. We find evidence for the formation of ground-state 85Rb2 molecules in low vibrational levels (v≤slant 20) with a maximal rate of 104 s-1, induced by short-range photoassociation by the fiber laser followed by spontaneous emission. When this laser is used to set up a dipole trap, we measure an atomic loss rate at a wavelength far from the PA resonances, only four times smaller than that observed at a PA resonance wavelength. This work may have important consequences for atom trapping using lasers around the conventional 1064 nm wavelength.

Scaling from single molecule to macroscopic adhesion at polymer/metal interfaces.

PubMed

Utzig, Thomas; Raman, Sangeetha; Valtiner, Markus

2015-03-10

Understanding the evolution of macroscopic adhesion based on fundamental molecular interactions is crucial to designing strong and smart polymer/metal interfaces that play an important role in many industrial and biomedical applications. Here we show how macroscopic adhesion can be predicted on the basis of single molecular interactions. In particular, we carry out dynamic single molecule-force spectroscopy (SM-AFM) in the framework of Bell-Evans' theory to gain information about the energy barrier between the bound and unbound states of an amine/gold junction. Furthermore, we use Jarzynski's equality to obtain the equilibrium ground-state energy difference of the amine/gold bond from these nonequilibrium force measurements. In addition, we perform surface forces apparatus (SFA) experiments to measure macroscopic adhesion forces at contacts where approximately 10(7) amine/gold bonds are formed simultaneously. The SFA approach provides an amine/gold interaction energy (normalized by the number of interacting molecules) of (36 ± 1)k(B)T, which is in excellent agreement with the interaction free energy of (35 ± 3)k(B)T calculated using Jarzynski's equality and single-molecule AFM experiments. Our results validate Jarzynski's equality for the field of polymer/metal interactions by measuring both sides of the equation. Furthermore, the comparison of SFA and AFM shows how macroscopic interaction energies can be predicted on the basis of single molecular interactions, providing a new strategy to potentially predict adhesive properties of novel glues or coatings as well as bio- and wet adhesion.

Molecular Dynamics Simulation of Carbon Nanotube Based Gears

NASA Technical Reports Server (NTRS)

Han, Jie; Globus, Al; Jaffe, Richard; Deardorff, Glenn; Chancellor, Marisa K. (Technical Monitor)

1996-01-01

We used molecular dynamics to investigate the properties and design space of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with C60. A modified, parallelized version of Brenner's potential was used to model interatomic forces within each molecule. A Leonard-Jones 6-12 potential was used for forces between molecules. One gear was powered by forcing the atoms near the end of the buckytube to rotate, and a second gear was allowed.to rotate by keeping the atoms near the end of its buckytube on a cylinder. The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. A number of gear and gear/shaft configurations were simulated. Cases in vacuum and with an inert atmosphere were examined. In an extension to molecular dynamics technology, some simulations used a thermostat on the atmosphere while the hydrocarbon gear's temperature was allowed to fluctuate. This models cooling the gears with an atmosphere. Results suggest that these gears can operate at up to 50-100 gigahertz in a vacuum or inert atmosphere at room temperature. The failure mode involves tooth slip, not bond breaking, so failed gears can be returned to operation by lowering temperature and/or rotation rate. Videos and atomic trajectory files in xyz format are presented.

Detection of the barium daughter in 136Xe -->136Ba + 2e- by in situ single-molecule fluorescence imaging

NASA Astrophysics Data System (ADS)

Nygren, David

2015-10-01

To proceed toward effective ``discovery class'' ton-scale detectors in the search for neutrino-less double beta decay, a robust technique for rejection of all radioactivity-induced backgrounds is urgently needed. An efficient technique for detection of the barium daughter in the decay 136Xe -->136Ba + 2e- would provide a long-sought pathway toward this goal. Single-molecule fluorescent imaging appears to offer a new way to detect the barium daughter atom, which emerges naturally in an ionized state in pure xenon. A doubly charged barium ion can initiate a chelation process with a non-fluorescent precursor molecule, leading to a highly fluorescent complex. Repeated photo-excitation of the complex can reveal both presence and location of a single ionized atom with high precision and selectivity. Detection within the active volume of a xenon gas Time Projection Chamber operating at high pressure would be automatic, and with a capability for redundant confirmation.

Broadband THz Generation and Detection at 10 nm Scale

NASA Astrophysics Data System (ADS)

Ma, Yanjun; Huang, Mengchen; Levy, Jeremy; Ryu, Sangwoo; Wung Bark, Chung; Eom, Chang-Beom

2013-03-01

The terahertz region of the electromagnetic spectrum (0.1 THz-10 THz) probes a wealth of information relevant for material, biological, medical and pharmaceutical sciences, as well as applications in chemical sensing and homeland security. To date, there have been no methods capable of controlling THz radiation at scales relevant for single molecules. Here we report the generation and detection of broadband terahertz radiation from 10-nm-scale nanojunctions which are ''sketched'' at the interface of LaAlO3/SrTiO3 (LAO/STO) heterostructure with a conductive atomic force microscope (c-AFM) tip. The nonresonant χ (3) process is characterized for a single nanojunction structure, which is nonlienar electronic response to both the static field cross the junction and the optical field illuminated the junction. The same mechanism can result in the generation and detection of broadband THz radiation. This unprecedented control of terahertz radiation, on a scale of four orders of magnitude smaller than the diffraction limit, creates a pathway toward ultra-high-resolution THz imaging, single-molecule fingerprinting, spectroscopic characterization of catalysts, and other applications. The authors acknowledge support from AFOSR - FA9550-12-1-0268 (J. L.), AFOSR FA9550-12-1-0342 (C. -B. E.) and the National Science Foundation through grants DMR-1104191 (J. L.) and DMR-1234096 (C. -B. E.).

Study of water diffusion on single-supported bilayer lipid membranes by quasielastic neutron scattering

NASA Astrophysics Data System (ADS)

Bai, M.; Miskowiec, A.; Hansen, F. Y.; Taub, H.; Jenkins, T.; Tyagi, M.; Diallo, S. O.; Mamontov, E.; Herwig, K. W.; Wang, S.-K.

2012-05-01

High-energy-resolution quasielastic neutron scattering has been used to elucidate the diffusion of water molecules in proximity to single bilayer lipid membranes supported on a silicon substrate. By varying sample temperature, level of hydration, and deuteration, we identify three different types of diffusive water motion: bulk-like, confined, and bound. The motion of bulk-like and confined water molecules is fast compared to those bound to the lipid head groups (7-10 H2O molecules per lipid), which move on the same nanosecond time scale as H atoms within the lipid molecules.

Crystal structure and conformational analysis of s-cis-(acetylacetonato)(ethylenediamine-N,N'-diacetato)-chromium(III): development of vibrationally optimized force field (VOFF).

PubMed

Choi, Jong-Ha; Niketić, Svetozar R; Djordjević, Ivana; Clegg, William; Harrington, Ross W

2012-05-01

The crystal structure of [Cr(edda)(acac)] (edda = ethylediamine-N,N'-diacetate; acac = acetylacetonato) has been determined by a single crystal X-ray diffraction study at 150 K. The chromium ion is in a distorted octahedral environment coordinated by two N and two O atoms of chelating edda and two O atoms of acac, resulting in s-cis configuration. The complex crystallizes in the space group P2(1)/c of the monoclinic system in a cell of dimensions a = 10.2588(9), b = 15.801(3), c = 8.7015(11) Å, β =101.201(9)° and Z = 4. The mean Cr-N(edda), Cr-O(edda) and Cr-O(acac) bond distances are 2.0829(14), 1.9678(11) and 1.9477(11) Å while the angles O-Cr-O of edda and O-Cr-O of acac are 171.47(5) and 92.72(5)°, respectively. The crystal structure is stabilized by N-H···O hydrogen bonds linking [Cr(edda)(acac)] molecules in distinct linear strands. The visible electronic and IR spectroscopic properties are also discussed. An improved, physically more realistic force field, Vibrationally Optimized Force Field (VOFF), capable of reproducing structural and vibrational properties of [Cr(edda)(acac)] was developed and its transferability demonstrated on selected chromium(III) complexes with similar ligands.

Atomic Force Microscopy Studies on DNA Structural Changes Induced by Vincristine Sulfate and Aspirin

NASA Astrophysics Data System (ADS)

Zhu, Yi; Zeng, Hu; Xie, Jianming; Ba, Long; Gao, Xiang; Lu, Zuhong

2004-04-01

We report that atomic force microscopy (AFM) studies on structural variations of a linear plasmid DNA interact with various concentrations of vincristine sulfate and aspirin. The different binding images show that vincrinstine sulfate binding DNA chains caused some loops and cleavages of the DNA fragments, whereas aspirin interaction caused the width changes and conformational transition of the DNA fragments. Two different DNA structural alternations could be explained by the different mechanisms of the interactions with these two components. Our work indicates that the AFM is a powerful tool in studying the interaction between DNA and small molecules.

Simultaneous Single-Molecule Force and Fluorescence Sampling of DNA Nanostructure Conformations Using Magnetic Tweezers.

PubMed

Kemmerich, Felix E; Swoboda, Marko; Kauert, Dominik J; Grieb, M Svea; Hahn, Steffen; Schwarz, Friedrich W; Seidel, Ralf; Schlierf, Michael

2016-01-13

We present a hybrid single-molecule technique combining magnetic tweezers and Förster resonance energy transfer (FRET) measurements. Through applying external forces to a paramagnetic sphere, we induce conformational changes in DNA nanostructures, which are detected in two output channels simultaneously. First, by tracking a magnetic bead with high spatial and temporal resolution, we observe overall DNA length changes along the force axis. Second, the measured FRET efficiency between two fluorescent probes monitors local conformational changes. The synchronized orthogonal readout in different observation channels will facilitate deciphering the complex mechanisms of biomolecular machines.

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

Das, Kaushik, E-mail: kaushikdas2089@gmail.com; Kundu, Sarathi

Long chain fatty acid molecules (e.g., stearic and behenic acids) form a monolayer on water surface in the presence of Ba{sup 2+} ions at low subphase pH (≈ 5.5) and remain as a monolayer before collapse generally occurs at higher surface pressure (π{sub c} > 50 mN/m). Monolayer formation is verified from the surface pressure vs. area per molecule (π-A) isotherms and also from the atomic force microscopy (AFM) analysis of the films deposited by single upstroke of hydrophilic Si (001) substrate through the monolayer covered water surface. At high subphase pH (≈ 9.5), barium stearate molecules form multilayer structuremore » at lower surface pressure which is verified from the π-A isotherms and AFM analysis of the film deposited at 25 mN/m. Such monolayer to multilayer structure formation or monolayer collapse at lower surface pressure is unusual as at this surface pressure generally fatty acid salt molecules form a monolayer on the water surface. Formation of bidentate chelate coordination in the metal containing headgroups is the reason for such monolayer to multilayer transition. However, for longer chain barium behenate molecules only monolayer structure is maintained at that high subphase pH (≈ 9.5) due to the presence of relatively more tail-tail hydrophobic interaction.« less

Synthesis and characterization of triangulene

NASA Astrophysics Data System (ADS)

Pavliček, Niko; Mistry, Anish; Majzik, Zsolt; Moll, Nikolaj; Meyer, Gerhard; Fox, David J.; Gross, Leo

2017-05-01

Triangulene, the smallest triplet-ground-state polybenzenoid (also known as Clar's hydrocarbon), has been an enigmatic molecule ever since its existence was first hypothesized. Despite containing an even number of carbons (22, in six fused benzene rings), it is not possible to draw Kekulé-style resonant structures for the whole molecule: any attempt results in two unpaired valence electrons. Synthesis and characterization of unsubstituted triangulene has not been achieved because of its extreme reactivity, although the addition of substituents has allowed the stabilization and synthesis of the triangulene core and verification of the triplet ground state via electron paramagnetic resonance measurements. Here we show the on-surface generation of unsubstituted triangulene that consists of six fused benzene rings. The tip of a combined scanning tunnelling and atomic force microscope (STM/AFM) was used to dehydrogenate precursor molecules. STM measurements in combination with density functional theory (DFT) calculations confirmed that triangulene keeps its free-molecule properties on the surface, whereas AFM measurements resolved its planar, threefold symmetric molecular structure. The unique topology of such non-Kekulé hydrocarbons results in open-shell π-conjugated graphene fragments that give rise to high-spin ground states, potentially useful in organic spintronic devices. Our generation method renders manifold experiments possible to investigate triangulene and related open-shell fragments at the single-molecule level.

ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs

NASA Astrophysics Data System (ADS)

Cleves, Ann E.; Jain, Ajay N.

2017-05-01

We introduce the ForceGen method for 3D structure generation and conformer elaboration of drug-like small molecules. ForceGen is novel, avoiding use of distance geometry, molecular templates, or simulation-oriented stochastic sampling. The method is primarily driven by the molecular force field, implemented using an extension of MMFF94s and a partial charge estimator based on electronegativity-equalization. The force field is coupled to algorithms for direct sampling of realistic physical movements made by small molecules. Results are presented on a standard benchmark from the Cambridge Crystallographic Database of 480 drug-like small molecules, including full structure generation from SMILES strings. Reproduction of protein-bound crystallographic ligand poses is demonstrated on four carefully curated data sets: the ConfGen Set (667 ligands), the PINC cross-docking benchmark (1062 ligands), a large set of macrocyclic ligands (182 total with typical ring sizes of 12-23 atoms), and a commonly used benchmark for evaluating macrocycle conformer generation (30 ligands total). Results compare favorably to alternative methods, and performance on macrocyclic compounds approaches that observed on non-macrocycles while yielding a roughly 100-fold speed improvement over alternative MD-based methods with comparable performance.

Self-assembled molecular magnets on patterned silicon substrates: bridging bio-molecules with nanoelectronics.

PubMed

Chang, Chia-Ching; Sun, Kien Wen; Lee, Shang-Fan; Kan, Lou-Sing

2007-04-01

The paper reports the methods of preparing molecular magnets and patterning of the molecules on a semiconductor surface. A highly magnetically aligned metallothionein containing Mn and Cd (Mn,Cd-MT-2) is first synthesized, and the molecules are then placed into nanopores prepared on silicon (001) surfaces using electron beam lithography and reactive ion-etching techniques. We have observed the self-assemble growth of the MT molecules on the patterned Si surface such that the MT molecules have grown into rod or ring type three-dimensional nanostructures, depending on the patterned nanostructures on the surface. We also provide scanning electron microscopy, atomic force microscopy, and magnetic force microscope studies of the molecular nanostructures. This engineered molecule shows molecular magnetization and is biocompatible with conventional semiconductors. These features make Mn,Cd-MT-2 a good candidate for biological applications and sensing sources of new nanodevices. Using molecular self-assembly and topographical patterning of the semiconductor substrate, we can close the gap between bio-molecules and nanoelectronics built into the semiconductor chip.

Nanobubbles do not sit alone at the solid-liquid interface.

PubMed

Peng, Hong; Hampton, Marc A; Nguyen, Anh V

2013-05-21

The unexpected stability and anomalous contact angle of gaseous nanobubbles at the hydrophobic solid-liquid interface has been an issue of debate for almost two decades. In this work silicon-nitride tipped AFM cantilevers are used to probe the highly ordered pyrolytic graphite (HOPG)-water interface with and without solvent-exchange (a common nanobubble production method). Without solvent-exchange the force obtained by the single force and force mapping techniques is consistent over the HOPG atomic layers and described by DLVO theory (strong EDL repulsion). With solvent-exchange the force is non-DLVO (no EDL repulsion) and the range of the attractive jump-in (>10 nm) over the surface is grouped into circular areas of longer range, consistent with nanobubbles, and the area of shorter range. The non-DLVO nature of the area between nanobubbles suggests that the interaction is no longer between a silicon-nitride tip and HOPG. Interfacial gas enrichment (IGE) covering the entire area between nanobubbles is suggested to be responsible for the non-DLVO forces. The absence of EDL repulsion suggests that both IGE and nanobubbles are not charged. The coexistence of nanobubbles and IGE provides further evidence of nanobubble stability by dynamic equilibrium. The IGE cannot be removed by contact mode scanning of a cantilever tip in pure water, but in a surfactant (SDS) solution the mechanical action of the tip and the chemical action of the surfactant molecules can successfully remove the enrichment. Strong EDL repulsion between the tip and nanobubbles/IGE in surfactant solutions is due to the polar heads of the adsorbed surfactant molecules.

Real-space identification of intermolecular bonding with atomic force microscopy.

PubMed

Zhang, Jun; Chen, Pengcheng; Yuan, Bingkai; Ji, Wei; Cheng, Zhihai; Qiu, Xiaohui

2013-11-01

We report a real-space visualization of the formation of hydrogen bonding in 8-hydroxyquinoline (8-hq) molecular assemblies on a Cu(111) substrate, using noncontact atomic force microscopy (NC-AFM). The atomically resolved molecular structures enable a precise determination of the characteristics of hydrogen bonding networks, including the bonding sites, orientations, and lengths. The observation of bond contrast was interpreted by ab initio density functional calculations, which indicated the electron density contribution from the hybridized electronic state of the hydrogen bond. Intermolecular coordination between the dehydrogenated 8-hq and Cu adatoms was also revealed by the submolecular resolution AFM characterization. The direct identification of local bonding configurations by NC-AFM would facilitate detailed investigations of intermolecular interactions in complex molecules with multiple active sites.

Direct Visualization of Barrier Crossing Dynamics in a Driven Optical Matter System.

PubMed

Figliozzi, Patrick; Peterson, Curtis W; Rice, Stuart A; Scherer, Norbert F

2018-04-25

A major impediment to a more complete understanding of barrier crossing and other single-molecule processes is the inability to directly visualize the trajectories and dynamics of atoms and molecules in reactions. Rather, the kinetics are inferred from ensemble measurements or the position of a transducer ( e. g., an AFM cantilever) as a surrogate variable. Direct visualization is highly desirable. Here, we achieve the direct measurement of barrier crossing trajectories by using optical microscopy to observe position and orientation changes of pairs of Ag nanoparticles, i. e. passing events, in an optical ring trap. A two-step mechanism similar to a bimolecular exchange reaction or the Michaelis-Menten scheme is revealed by analysis that combines detailed knowledge of each trajectory, a statistically significant number of repetitions of the passing events, and the driving force dependence of the process. We find that while the total event rate increases with driving force, this increase is due to an increase in the rate of encounters. There is no drive force dependence on the rate of barrier crossing because the key motion for the process involves a random (thermal) radial fluctuation of one particle allowing the other to pass. This simple experiment can readily be extended to study more complex barrier crossing processes by replacing the spherical metal nanoparticles with anisotropic ones or by creating more intricate optical trapping potentials.

Diagnosing the Internal Architecture of Zeolite Ferrierite

PubMed Central

Schmidt, Joel E.; Hendriks, Frank C.; Lutz, Martin; Post, L. Christiaan; Fu, Donglong

2017-01-01

Abstract Large crystals of zeolite ferrierite (FER) are important model systems for spatially resolved catalysis and diffusion studies, though there is considerable variation in crystal habit depending on the chemical composition and employed synthesis conditions. A synergistic combination of techniques has been applied, including single crystal X‐ray diffraction, high‐temperature in situ confocal fluorescence microscopy, fluorescent probe molecules, wide‐field microscopy and atomic force microscopy to unravel the internal architecture of three distinct FER zeolites. Pyrolyzed template species can be used as markers for the 8‐membered ring direction as they are trapped in the terraced roof of the FER crystals. This happens as the materials grow in a layer‐by‐layer, defect‐free manner normal to the large crystal surface, and leads to a facile method to diagnose the pore system orientation, which avoids tedious single crystal X‐ray diffraction experiments. PMID:28809081

Characterization of the interaction between diferric transferrin and transferrin receptor 2 by functional assays and atomic force microscopy*

PubMed Central

Ikuta, Katsuya; Yersin, Alexandre; Ikai, Atsushi; Aisen, Philip; Kohgo, Yutaka

2010-01-01

Transferrin receptor (TfR2), a homologue of classical transferrin receptor 1 (TfR1), is found in two isoforms, α and β. Like TfR1, TfR2α is a type II membrane protein, but the β form lacks transmembrane portions and therefore is likely to be an intracellular protein. To investigate the functional properties of TfR2α we expressed the protein with FLAG-tagging in transferrin receptor-deficient Chinese hamster ovary cells. The association constant for binding of diferric transferrin (Tf) to TfR2α is 5.6 × 106 M−1, which is about 50 times lower than that of TfR1, with correspondingly reduced rates of iron uptake. Evidence for Tf internalization and recycling via TfR2α without degradation, as in the TfR1 pathway, was also found. The interaction of TfR2α with Tf was further investigated using atomic force microscopy (AFM), a powerful tool for investigation of the interaction between ligand and receptor at the single molecule level on the living cell surface. Dynamic force microscopy reveals a difference in the interactions of Tf with TfR2α and TfR1, with Tf-TfR1 unbinding characterized by 2 energy barriers, while only one is present for Tf-TfR2. We speculate that this difference may reflect Tf binding to TfR2α by a single lobe, whereas two lobes of Tf participate in binding to TfR1. The difference in the binding properties of Tf to TfR1 and TfR2α may help account for the different physiological roles of the two receptors. PMID:20096706

Improved localization of cellular membrane receptors using combined fluorescence microscopy and simultaneous topography and recognition imaging

NASA Astrophysics Data System (ADS)

Duman, M.; Pfleger, M.; Zhu, R.; Rankl, C.; Chtcheglova, L. A.; Neundlinger, I.; Bozna, B. L.; Mayer, B.; Salio, M.; Shepherd, D.; Polzella, P.; Moertelmaier, M.; Kada, G.; Ebner, A.; Dieudonne, M.; Schütz, G. J.; Cerundolo, V.; Kienberger, F.; Hinterdorfer, P.

2010-03-01

The combination of fluorescence microscopy and atomic force microscopy has a great potential in single-molecule-detection applications, overcoming many of the limitations coming from each individual technique. Here we present a new platform of combined fluorescence and simultaneous topography and recognition imaging (TREC) for improved localization of cellular receptors. Green fluorescent protein (GFP) labeled human sodium-glucose cotransporter (hSGLT1) expressed Chinese Hamster Ovary (CHO) cells and endothelial cells (MyEnd) from mouse myocardium stained with phalloidin-rhodamine were used as cell systems to study AFM topography and fluorescence microscopy on the same surface area. Topographical AFM images revealed membrane features such as lamellipodia, cytoskeleton fibers, F-actin filaments and small globular structures with heights ranging from 20 to 30 nm. Combined fluorescence and TREC imaging was applied to detect density, distribution and localization of YFP-labeled CD1d molecules on α-galactosylceramide (αGalCer)-loaded THP1 cells. While the expression level, distribution and localization of CD1d molecules on THP1 cells were detected with fluorescence microscopy, the nanoscale distribution of binding sites was investigated with molecular recognition imaging by using a chemically modified AFM tip. Using TREC on the inverted light microscope, the recognition sites of cell receptors were detected in recognition images with domain sizes ranging from ~ 25 to ~ 160 nm, with the smaller domains corresponding to a single CD1d molecule.

Improved localization of cellular membrane receptors using combined fluorescence microscopy and simultaneous topography and recognition imaging.

PubMed

Duman, M; Pfleger, M; Zhu, R; Rankl, C; Chtcheglova, L A; Neundlinger, I; Bozna, B L; Mayer, B; Salio, M; Shepherd, D; Polzella, P; Moertelmaier, M; Kada, G; Ebner, A; Dieudonne, M; Schütz, G J; Cerundolo, V; Kienberger, F; Hinterdorfer, P

2010-03-19

The combination of fluorescence microscopy and atomic force microscopy has a great potential in single-molecule-detection applications, overcoming many of the limitations coming from each individual technique. Here we present a new platform of combined fluorescence and simultaneous topography and recognition imaging (TREC) for improved localization of cellular receptors. Green fluorescent protein (GFP) labeled human sodium-glucose cotransporter (hSGLT1) expressed Chinese Hamster Ovary (CHO) cells and endothelial cells (MyEnd) from mouse myocardium stained with phalloidin-rhodamine were used as cell systems to study AFM topography and fluorescence microscopy on the same surface area. Topographical AFM images revealed membrane features such as lamellipodia, cytoskeleton fibers, F-actin filaments and small globular structures with heights ranging from 20 to 30 nm. Combined fluorescence and TREC imaging was applied to detect density, distribution and localization of YFP-labeled CD1d molecules on alpha-galactosylceramide (alphaGalCer)-loaded THP1 cells. While the expression level, distribution and localization of CD1d molecules on THP1 cells were detected with fluorescence microscopy, the nanoscale distribution of binding sites was investigated with molecular recognition imaging by using a chemically modified AFM tip. Using TREC on the inverted light microscope, the recognition sites of cell receptors were detected in recognition images with domain sizes ranging from approximately 25 to approximately 160 nm, with the smaller domains corresponding to a single CD1d molecule.

The Use of Ultrashort Picosecond Laser Pulses to Generate Quantum Optical Properties of Single Molecules in Biophysics

NASA Astrophysics Data System (ADS)

Ly, Sonny

Generation of quantum optical states from ultrashort laser-molecule interactions have led to fascinating discoveries in physics and chemistry. In recent years, these interactions have been extended to probe phenomena in single molecule biophysics. Photons emitted from a single fluorescent molecule contains important properties about how the molecule behave and function in that particular environment. Analysis of the second order coherence function through fluorescence correlation spectroscopy plays a pivotal role in quantum optics. At very short nanosecond timescales, the coherence function predicts photon antibunching, a purely quantum optical phenomena which states that a single molecule can only emit one photon at a time. Photon antibunching is the only direct proof of single molecule emission. From the nanosecond to microsecond timescale, the coherence function gives information about rotational diffusion coefficients, and at longer millisecond timescales, gives information regarding the translational diffusion coefficients. In addition, energy transfer between molecules from dipole-dipole interaction results in FRET, a highly sensitive method to probe conformational dynamics at nanometer distances. Here I apply the quantum optical techniques of photon antibunching, fluorescence correlation spectroscopy and FRET to probe how lipid nanodiscs form and function at the single molecule level. Lipid nanodiscs are particles that contain two apolipoprotein (apo) A-I circumventing a lipid bilayer in a belt conformation. From a technological point of view, nanodiscs mimics a patch of cell membrane that have recently been used to reconstitute a variety of membrane proteins including cytochrome P450 and bacteriorhodopsin. They are also potential drug transport vehicles due to its small and stable 10nm diameter size. Biologically, nanodiscs resemble to high degree, high density lipoproteins (HDL) in our body and provides a model platform to study lipid-protein interactions and their dynamic formation to lipoprotein particles without having to extract from human blood plasma. Although HDL has been studied extensively within the last thirty years, many questions still remain regarding the structure of apoA-I, the protein associated exclusively with it. Despite our ability to detect and image these nanodiscs by blotting, atomic force microscopy (AFM), or electron microscopy (EM), many basic properties such as their specific hydrated shape in solution, or the precise conformation of the apolipoproteins surrounding the particles are still unknown. The dynamic interactions of apoA-I with lipids are also rather poorly understood on a fundamental level, and are only characterized in bulk (biochemical blotting) or stationary methods (AFM, EM), making it impossible to study individual steps with high spatial or temporal resolution.

Enhancing optical nonreciprocity by an atomic ensemble in two coupled cavities

NASA Astrophysics Data System (ADS)

Song, L. N.; Wang, Z. H.; Li, Yong

2018-05-01

We study the optical nonreciprocal propagation in an optical molecule of two coupled cavities with one of them interacting with a two-level atomic ensemble. The effect of increasing the number of atoms on the optical isolation ratio of the system is studied. We demonstrate that the significant nonlinearity supplied by the coupling of the atomic ensemble with the cavity leads to the realization of greatly-enhanced optical nonreciprocity compared with the case of single atom.