CiteULike: Tag force

A unified geometric approach to modeling and control of constrained mechanical systems

Guanfeng Liu — 2005-04-19T18:00:12-00:00

Robotics and Automation, IEEE Transactions on, Vol. 18, No. 4. (2002), pp. 574-587.

Dynamic control of constrained mechanical systems, such as robotic manipulators under end-effector constraints, parallel manipulators, and multifingered robotic hands under closure constraints have been classic problems in robotics research. In this paper, we provide a unified geometric framework for modeling, analysis, and control of constrained mechanical systems. Starting with the constraint, we define two canonical subspaces, namely the subspace of constraint forces and the tangent space of the constraint manifold for holonomic constraint. Using the kinetic energy metric, we define the remaining subspaces and show explicitly the relations among these subspaces. We project the Euler-Lagrange equation of a constrained mechanical system into two orthogonal components and give geometric and physical interpretations of the projected equations. Based on the projected equations, a unified and asymptotically stable hybrid position/force-control algorithm is proposed, along with experimental results for several practical examples. In the case of nonholonomic constraints, we show that the equations can be projected to the distribution/codistribution associated with the constraints and the control law reduces to hybrid velocity/force control.

Extracellular pH and tension during ischemia in the isolated rabbit ventricle.

GS Couper — 2006-06-02T17:10:44-00:00

Am J Physiol, Vol. 247, No. 6 Pt 2. (December 1984)

To investigate the factors determining the rate of H+ accumulation during early ischemia, miniature intramyocardial pH electrodes (tip diam 0.2-0.5 mm) were used to record extracellular pH (pHo) in the isolated arterially perfused rabbit interventricular septum. Changes in pHo and the rate of fall of tension during global ischemia were compared under control conditions (37 degrees C, heart rate 75 beats/min) and after exposure to the following interventions: reduced heart rate (36 beats/min), hypothermia (27 degrees C), verapamil (0.5 microM), reduced extracellular Ca2+ concentration [( Ca2+]o 0.5 mM), norepinephrine (0.5 microM) in normal and catecholamine-depleted preparations, norepinephrine and reduced [Ca2+]o, and theophylline (4 mM). Under control conditions pHo declined by 0.61-0.73 pH units after 10 min of ischemia. The negative inotropic interventions and reduced temperature significantly decreased [H+]o accumulation during ischemia. Positive inotropic interventions did not affect the rate of [H+]o accumulation during ischemia except in reserpinized preparations. All of the interventions except for reduced temperature significantly altered the relationship between tension and pHo during ischemia.

Absence of a relationship between extracellular potassium accumulation and contractile failure in the ischemic or hypoxic rabbit heart.

SC Webb — 2006-06-02T17:08:28-00:00

Adv Myocardiol, Vol. 6 (1985), pp. 405-415.

Ischemia and hypoxia both cause a rapid loss of potassium from myocardial cells. We have investigated the relationship between the accumulation of potassium in the extracellular fluid and the early loss of contractility. Experiments were performed on the isolated rabbit heart perfused with physiological saline at 36 degrees C, paced at 3 Hz. Tension was recorded from the apex. Extracellular potassium concentration [( K+]o) was recorded with small ion-selective electrodes. After the onset of global ischemia, [K+]o rose within 15 sec and reached 9.5 +/- 1.1 mmoles/liter after 5 min. Developed tension (T) fell to 9 +/- 2% of control over the same period. During substrate-free hypoxia, T declined at a similar rate, and [K+]o rose slowly to 5.5 +/- 0.1 mmoles/liter after 5 min. The relationship between [K]o and T during normal perfusion and oxygenation was investigated by incrementally increasing the perfusate [K+]. T dropped to 78.6 +/- 4.5% of control at a [K+]o of 9 mmoles/liter. Comparison of the relationship between [K+]o and T during high-potassium perfusion, ischemia, and hypoxia shows that extracellular potassium accumulation per se makes almost no contribution to the decline of contractile function in ischemia or hypoxia. (Values are means +/- S.E., N = 5.)

Defibrillation depresses heart sarcoplasmic reticulum calcium pump: a mechanism of postshock dysfunction.

DL Jones — 2006-11-13T23:00:27-00:00

Am J Physiol, Vol. 274, No. 1 Pt 2. (January 1998)

Presently, the only therapy for ventricular fibrillation is delivery of high-voltage shocks. Despite "successful defibrillation," patients may have poor cardiac contractility, the mechanisms of which are unknown. Intracellular Ca2+ handling by the sarcoplasmic reticulum (SR) plays a major role in contractility. We tested the hypothesis that defibrillation shocks interfere with Ca2+ transport function of cardiac SR. Rats anesthetized with pentobarbital sodium had bilateral electrodes implanted subcutaneously for transthoracic shocks. A series of 10 shocks, 10 s apart, at 0-250 V was delivered from a trapezoidal defibrilator. The hearts were rapidly removed, SR-enriched membrane vesicles were isolated, and ATP-dependent Ca2+ uptake and Ca(2+)-stimulated ATP hydrolysis were determined. There was a marked, shock-related decline in Ca2+ uptake, whereas adenosinetriphosphatase activity remained unaltered. The polypeptide compositions were similar in control and shocked SR. In Langendorff hearts, shocks also decreased contractility and slowed relaxation. These data indicate that shocks with current densities similar to defibrillation depress Ca(2+)-pumping function of cardiac SR because of uncoupling of ATP hydrolysis and Ca2+ transport. Shock-induced impairment of Ca2+ pump function may underlie postshock myocardial dysfunction.

Effect of stretch on contraction and the Ca2+ transient in ferret ventricular muscles during hypoxia and acidosis.

K Hongo — 2006-06-13T00:06:18-00:00

Am J Physiol, Vol. 269, No. 3 Pt 1. (September 1995)

The effect of stretch on cardiac muscle contraction and the Ca2+ transient was studied during hypoxia and acidosis in isolated ferret ventricular muscles. In control conditions, a maintained stretch produced an immediate increase in tension followed by a slow increase in tension and the Ca2+ transient. A stretch between contractions (diastolic stretch) caused only a slow increase in tension and the Ca2+ transient, whereas a stretch during the period of contraction (systolic stretch) produced an immediate increase in tension followed by a small slow increase in tension and the Ca2+ transient. In hypoxia, the immediate percent increase in tension was the same as in control. However, the slow increase was smaller during all three types of stretch. In acidosis, the immediate percent increase in tension was larger than in control. The slow change was the same during maintained stretch. However, the slow increase in tension was smaller during diastolic stretch and larger during systolic stretch. Thus the stretch-dependent increase in contraction is inhibited during hypoxia and modulated by acidosis.

The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations.

Siewert Marrink — 2007-06-23T13:08:19-00:00

Journal of Physical Chemistry B (15 June 2007)

We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of possible interaction levels of the coarse-grained sites has increased compared to those of the previous model. Application of the new model to lipid bilayers shows an improved behavior in terms of the stress profile across the bilayer and the tendency to form pores. An extension of the force field now also allows the simulation of planar (ring) compounds, including sterols. Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations.

Force-distance curves by atomic force microscopy

B Cappella — 2008-04-21T16:09:32-00:00

Surface Science Reports, Vol. 34, No. 1-3. (1999), pp. 1-104.

Atomic force microscopy (AFM) force-distance curves have become a fundamental tool in several fields of research, such as surface science, materials engineering, biochemistry and biology. Furthermore, they have great importance for the study of surface interactions from a theoretical point of view. Force-distance curves have been employed for the study of numerous materials properties and for the characterization of all the known kinds of surface forces. Since 1989, several techniques of acquisition and analysis have arisen. An increasing number of systems, presenting new kinds of forces, have been analyzed. AFM force-distance curves are routinely used in several kinds of measurement, for the determination of elasticity. Hamaker constants, surface charge densities, and degrees of hydrophobicity. The present review is designed to indicate the theoretical background of AFM force-distance curves as well as to present the great variety of measurements that can be performed with this tool. Section 1 is a general introduction to AFM force-distance curves. In Sections 2-4 the fundamentals of the theories concerning the three regions of force-distance curves are summarized. In particular, Section 2 contains a review of the techniques employed for the characterization of the elastic properties of materials. After an overview of calibration problems (Section 5), the different forces that can be measured with AFM force-distance curves are discussed. Capillary, Coulomb, Van der Waals, double-layer, solvation, hydration, hydrophobic, specific and steric forces are considered. For each force the available theoretical aspects necessary for the comprehension of the experiments are provided. The main experiments concerning the measurements of such forces are listed, pointing out the experimental problems, the artifacts that are likely to affect the measurement, and the main established results. Experiments up to June 1998 are reviewed. Finally, in Section 7, techniques to acquire force-distance curves sequentially and to draw bidimensional maps of different parameters are listed.

Force-induced bidirectional stepping of cytoplasmic Dynein.

A Gennerich — 2007-12-24T03:54:09-00:00

Cell, Vol. 131, No. 5. (30 November 2007), pp. 952-965.

Cytoplasmic dynein is a minus-end-directed microtubule motor whose mechanism of movement remains poorly understood. Here, we use optical tweezers to examine the force-dependent stepping behavior of yeast cytoplasmic dynein. We find that dynein primarily advances in 8 nm increments but takes other sized steps (4-24 nm) as well. An opposing force induces more frequent backward stepping by dynein, and the motor walks backward toward the microtubule plus end at loads above its stall force of 7 pN. Remarkably, in the absence of ATP, dynein steps processively along microtubules under an external load, with less force required for minus-end- than for plus-end-directed movement. This nucleotide-independent walking reveals that force alone can drive repetitive microtubule detachment-attachment cycles of dynein's motor domains. These results suggest a model for how dynein's two motor domains coordinate their activities during normal processive motility and provide new clues for understanding dynein-based motility in living cells.

Measurement of the force-velocity relation for growing microtubules.

M Dogterom — 2007-06-22T14:30:51-00:00

Science, Vol. 278, No. 5339. (31 October 1997), pp. 856-860.

Forces generated by protein polymerization are important for various forms of cellular motility. Assembling microtubules, for instance, are believed to exert pushing forces on chromosomes during mitosis. The force that a single microtubule can generate was measured by attaching microtubules to a substrate at one end and causing them to push against a microfabricated rigid barrier at the other end. The subsequent buckling of the microtubules was analyzed to determine both the force on each microtubule end and the growth velocity. The growth velocity decreased from 1.2 micrometers per minute at zero force to 0.2 micrometer per minute at forces of 3 to 4 piconewtons. The force-velocity relation fits well to a decaying exponential, in agreement with theoretical models, but the rate of decay is faster than predicted.

Measurement of the Temperature Dependence of the Casimir-Polder Force

JM Obrecht — 2007-02-09T06:53:27-00:00

Physical Review Letters, Vol. 98, No. 6. (2007)

We report on the first measurement of a temperature dependence of the Casimir-Polder force. This measurement was obtained by positioning a nearly pure 87Rb Bose-Einstein condensate a few microns from a dielectric substrate and exciting its dipole oscillation. Changes in the collective oscillation frequency of the magnetically trapped atoms result from spatial variations in the surface-atom force. In our experiment, the dielectric substrate is heated up to 605 K, while the surrounding environment is kept near room temperature (310 K). The effect of the Casimir-Polder force is measured to be nearly 3 times larger for a 605 K substrate than for a room-temperature substrate, showing a clear temperature dependence in agreement with theory.

Stretching of Homopolymeric RNA Reveals Single-Stranded Helices and Base-Stacking

Yeonee Seol — 2007-06-19T17:45:20-00:00

Physical Review Letters, Vol. 98, No. 15. (2007)

We have found strong supporting evidence for the helical structures of single-stranded nucleic acids by stretching individual molecules of polyadenylic acid [poly(A)] and polycytidylic acid [poly(C)]. Analyzing the force versus extension data using a two-state elastic model in which random-coil domains alternate with rigid helical domains allows one to extract the thermodynamic and structural properties. In addition, it also yields moderate to low cooperativity of the helix-coil transition for poly(A) and poly(C), respectively.

Probing the relation between force--lifetime--and chemistry in single molecular bonds.

E Evans — 2008-03-29T21:10:56-00:00

Annu Rev Biophys Biomol Struct, Vol. 30 (2001), pp. 105-128.

On laboratory time scales, the energy landscape of a weak bond along a dissociation pathway is fully explored through Brownian-thermal excitations, and energy barriers become encoded in a dissociation time that varies with applied force. Probed with ramps of force over an enormous range of rates (force/time), this kinetic profile is transformed into a dynamic spectrum of bond rupture force as a function of loading rate. On a logarithmic scale in loading rate, the force spectrum provides an easy-to-read map of the prominent energy barriers traversed along the force-driven pathway and exposes the differences in energy between barriers. In this way, the method of dynamic force spectroscopy (DFS) is being used to probe the complex relation between force-lifetime-and chemistry in single molecular bonds. Most important, DFS probes the inner world of molecular interactions to reveal barriers that are difficult or impossible to detect in assays of near equilibrium dissociation but that determine bond lifetime and strength under rapid detachment. To use an ultrasensitive force probe as a spectroscopic tool, we need to understand the physics of bond dissociation under force, the impact of experimental technique on the measurement of detachment force (bond strength), the consequences of complex interactions in macromolecular bonds, and effects of multiply-bonded attachments.

Direct Measurement of Local Chromatin Fluidity Using Optical Trap Modulation Force Spectroscopy

T Roopa — 2007-05-10T07:28:35-00:00

Biophys. J., Vol. 91, No. 12. (15 December 2006), pp. 4632-4637.

Chromatin assembly is condensed by histone tail-tail interactions and other nuclear proteins into a highly compact structure. Using an optical trap modulation force spectroscopy, we probe the effect of tail interactions on local chromatin fluidity. Chromatin fibers, purified from mammalian cells, are tethered between a microscope coverslip and a glass micropipette. Mechanical unzipping of tail interactions, using the micropipette, lead to the enhancement of local fluidity. This is measured using an intensity-modulated optically trapped bead positioned as a force sensor on the chromatin fiber. Enzymatic digestion of the histone tail interactions of tethered chromatin fiber also leads to a similar increase in fluidity. Our experiments show that an initial increase in the local fluidity precedes chromatin decompaction, suggesting possible mechanisms by which chromatin-remodeling machines access regulatory sites. 10.1529/biophysj.106.086827

B-S Transition in Short Oligonucleotides

Julia Morfill — 2007-09-12T17:25:53-00:00

Biophys. J., Vol. 93, No. 7. (1 October 2007), pp. 2400-2409.

Stretching experiments with long double-stranded DNA molecules in physiological ambient revealed a force-induced transition at a force of 65 pN. During this transition between B-DNA and highly overstretched S-DNA the DNA lengthens by a factor of 1.7 of its B-form contour length. Here, we report the occurrence of this so-called B-S transition in short duplexes consisting of 30 basepairs. We employed atomic-force-microscope-based single molecule force spectroscopy to explore the unbinding mechanism of two short duplexes containing 30 or 20 basepairs by pulling at the opposite 5' termini. For a 30-basepair-long DNA duplex the B-S transition is expected to cause a length increase of 6.3 nm and should therefore be detectable. Indeed 30% of the measured force-extension curves exhibit a region of constant force (plateau) at 65 pN, which corresponds to the B-S transition. The observed plateaus show a length between 3 and 7 nm. This plateau length distribution indicates that the dissociation of a 30-basepair duplex mainly occurs during the B-S transition. In contrast, the measured force-extension curves for a 20-basepair DNA duplex exhibited rupture forces below 65 pN and did not show any evidence of a B-S transition. 10.1529/biophysj.107.106112

Micromachined piconewton force sensor for biophysics investigations

Steven Koch — 2007-02-03T09:23:18-00:00

Applied Physics Letters, Vol. 89, No. 17. (2006)

We describe a micromachined force sensor that is able to measure forces as small as 1 pN in both air and water. First, we measured the force field produced by an electromagnet on individual 2.8 µm magnetic beads glued to the sensor. By repeating with 11 different beads, we measured a 9% standard deviation in saturation magnetization. We next demonstrated that the sensor was fully functional when immersed in physiological buffer. These results show that the force sensors can be useful for magnetic force calibration and also for measurement of biophysical forces on chip. ©2006 American Institute of Physics

Predicting the rupture probabilities of molecular bonds in series.

G Neuert — 2007-09-25T09:28:41-00:00

Biophys J, Vol. 93, No. 4. (15 August 2007), pp. 1215-1223.

An assembly of two receptor ligand bonds in series will typically break at the weaker complex upon application of an external force. The rupture site depends highly on the binding potentials of both bonds and on the loading rate of the applied force. A model is presented that allows simulations of force-induced rupture of bonds in series at a given force and loading rate based on the natural dissociation rates kR0,S0 and the potential width DeltaxR,S of the reference and sample bonds. The model is especially useful for the analysis of differential force assay experiments. This is illustrated by experiments on molecular force balances consisting of two 30-bp oligonucleotide duplexes where kR0,S0 and DeltaxR,S have been determined for different single nucleotide mismatches. Furthermore, prediction of the rupture site of two bonds in series is demonstrated for DNA duplexes in combination with streptavidin/biotin and anti-digoxigenin/digoxigenin, respectively.

A micromachined DNA manipulation platform for the stretching and rotation of a single DNA molecule The preliminary results of the current paper were presented at the IEEE 17th International MEMS Conference (IEEE MEMS 2004), Maastricht, Netherlands, 25–29 Jan. 2004.

Chi Chiou — 2007-02-14T06:58:48-00:00

Journal of Micromechanics and Microengineering, Vol. 15, No. 1. (2005), pp. 109-117.

A micromachine-based DNA manipulation platform for stretching and rotation of a single DNA molecule is reported. The DNA molecule with a 2 nm diameter could be successfully manipulated using magnetic forces generated by arrayed microcoils fabricated by MEMS (micro-electro-mechanical systems) technology. Key platform technologies including localized DNA immobilization, microcoil fabrication and microfluidics, have been integrated to form the DNA magnetic tweezers. One end of a single DNA molecule is specifically bonded onto a magnetic bead and the other end onto a gold surface. It is then manipulated under a magnetic field generated by built-in hexagonally aligned microcoils. Design and simulation of the magnetic tweezers are carried out by using numerical software. A highly effective and strong binding method for the construction of two sticky ends of a DNA is developed, which is compatible with MEMS technologies. To quantify the magnitude of magnetic forces acting on the DNA, force calibration is performed and further verified by the worm-like chain (WLC) model. The measured DNA stretching forces are found to be in reasonable agreement with the theoretical values. We have successfully demonstrated the stretching and rotation of the tethered-bead DNA molecule linked to a gold pattern using the developed method. The spring constant of the DNA molecule is experimentally found to be about 10$^−8$–10$^−7$ N m$^−1$. The development of the proposed method could be useful for investigation of DNA biophysical properties.

Dynamic force spectroscopy of protein-DNA interactions by unzipping DNA.

SJ Koch — 2007-02-03T09:00:01-00:00

Phys Rev Lett, Vol. 91, No. 2. (11 July 2003)

We demonstrate the first site-specific single-molecule characterization of the prominent activation barrier for the disruption of a protein-DNA binding complex. We achieved this new capability by combining dynamic force spectroscopy with unzipping force analysis of protein association and used the combination to investigate restriction enzyme binding to specific DNA sites. Analysis revealed lifetimes and interaction distances for three protein-DNA interactions. This new method is able to distinguish protein-DNA binding complexes on a site-specific, single-molecule basis.

Forced Unfolding of Coiled-Coils in Fibrinogen by Single-Molecule AFM.

AE Brown — 2007-04-24T05:39:52-00:00

Biophys J, Vol. 92, No. 5. (1 March 2007)

Fibrinogen is a blood plasma protein that, after activation by thrombin, assembles into fibrin fibers that form the elastic network of blood clots. We used atomic force microscopy to study the forced unfolding of engineered linear oligomers of fibrinogen, and we show that forced extension of the oligomers produces sawtooth patterns with a peak-to-peak length consistent with the independent unfolding of the coiled-coils in a cooperative two-state manner. In contrast with force plateaus seen for myosin coiled-coils that suggested rapid refolding of myosin, Monte Carlo simulations of fibrinogen unfolding confirm that fibrinogen refolding is negligible on experimental timescales. The distinct behavior of fibrinogen seems to be due to its topologically complex coiled-coils and an interaction between fibrinogen's alphaC-domains and its central region.

Replication of DNA microarrays from zip code masters.

H Lin — 2007-02-20T05:53:30-00:00

J Am Chem Soc, Vol. 128, No. 10. (15 March 2006), pp. 3268-3272.

This report describes a mechanical method for efficient and accurate replication of DNA microarrays from a zip code master. The zip code master is a DNA array that defines the location of oligonucleotides consisting of two parts: a code sequence, which is complementary to one or more of the zip codes, and the functional sequence, which is terminated with biotin. Following hybridization of the zip code to the code sequence, a replica surface functionalized with streptavidin is brought into conformal contact with the surface of the master. When the two surfaces are separated, the functional and code sequences are transferred to the replica, and the zip code remains on the surface of the master. Using this approach it is possible to prepare replica arrays having any configuration from a single, universal master array. Here we demonstrate that this approach can be used to replicate master arrays having up to three different sequences, that feature sizes as small as 100 microm can be replicated, and that master arrays can be used to prepare multiple replicas.

Multi-Nanopore Force Spectroscopy for DNA Analysis

Carolina Tropini — 2007-02-20T05:45:29-00:00

Biophys. J., Vol. 92, No. 5. (1 March 2007), pp. 1632-1637.

The need for low-cost DNA sequence detection in clinical applications is driving development of new technologies. We demonstrate a method for detection of mutations in a DNA sequence purely by electronic means, and without need for fluorescent labeling. Our method uses an array of nanopores to perform synchronized single-molecule force spectroscopy measurements over many molecules in parallel, yielding detailed information on the kinetics of hundreds of molecule dissociations in a single measurement. 10.1529/biophysj.106.094060

Single-molecule experiments in vitro and in silico.

M Sotomayor — 2007-05-27T08:07:07-00:00

Science, Vol. 316, No. 5828. (25 May 2007), pp. 1144-1148.

Single-molecule force experiments in vitro enable the characterization of the mechanical response of biological matter at the nanometer scale. However, they do not reveal the molecular mechanisms underlying mechanical function. These can only be readily studied through molecular dynamics simulations of atomic structural models: "in silico" (by computer analysis) single-molecule experiments. Steered molecular dynamics simulations, in which external forces are used to explore the response and function of macromolecules, have become a powerful tool complementing and guiding in vitro single-molecule experiments. The insights provided by in silico experiments are illustrated here through a review of recent research in three areas of protein mechanics: elasticity of the muscle protein titin and the extracellular matrix protein fibronectin; linker-mediated elasticity of the cytoskeleton protein spectrin; and elasticity of ankyrin repeats, a protein module found ubiquitously in cells but with an as-yet unclear function.

Visualizing single DNA-bound proteins using DNA as a scanning probe

Maarten Noom — 2007-11-30T17:39:32-00:00

Nature Methods, Vol. 4, No. 12. (11 November 2007), pp. 1031-1036.

Pulling geometry-induced errors in single molecule force spectroscopy measurements.

C Ke — 2007-04-11T20:47:19-00:00

Biophys J, Vol. 92, No. 9. (1 May 2007)

In AFM-based single molecule force spectroscopy, it is tacitly assumed that the pulling direction coincides with the end-to-end vector of the molecule fragment being stretched. By systematically varying the position of the attachment point on the substrate relative to the AFM tip, we investigate empirically and theoretically the effect of the pulling geometry on force-extension characteristics of double-stranded DNA. We find that increasing the pulling angle can significantly lower the force of the characteristic overstretching transition and increase the width of the plateau feature beyond the canonical 70%. These effects, when neglected, can adversely affect the interpretation of measured force-extension relationships. We quantitatively evaluate force and extension errors originating from this "pulling angle effect" and stress the need to correct the pulling geometry when stretching rigid molecules with an AFM.

Three-dimensional force microscope: A nanometric optical tracking and magnetic manipulation system for the biomedical sciences

JK Fisher — 2007-04-19T18:12:46-00:00

Review of Scientific Instruments, Vol. 76, No. 5. (2005)

We report here the development of a three-dimensional (3D) magnetic force microscope for applying forces to and measuring responses of biological systems and materials. This instrument combines a conventional optical microscope with a free-floating or specifically bound magnetic bead used as a mechanical probe. Forces can be applied by the bead to microscopic structures of interest (specimens), while the reaction displacement of the bead is measured. This enables 3D mechanical manipulations and measurements to be performed on specimens in fluids. Force is generated by the magnetically permeable bead in reaction to fields produced by external electromagnets. The displacement is measured by interferometry using forward light scattered by the bead from a focused laser beam. The far-field interference pattern is imaged on a quadrant photodetector from which the 3D displacement can be computed over a limited range about the focal point. The bead and specimen are mounted on a 3D translation stage and feedback techniques are used to keep the bead within this limited range. We demonstrate the system with application to beads attached to cilia in human lung cell cultures. ©2005 American Institute of Physics

Thin-foil magnetic force system for high-numerical-aperture microscopy

JK Fisher — 2007-04-19T18:08:44-00:00

Review of Scientific Instruments, Vol. 77, No. 2. (2006)

Forces play a key role in a wide range of biological phenomena from single-protein conformational dynamics to transcription and cell division, to name a few. The majority of existing microbiological force application methods can be divided into two categories: those that can apply relatively high forces through the use of a physical connection to a probe and those that apply smaller forces with a detached probe. Existing magnetic manipulators utilizing high fields and high field gradients have been able to reduce this gap in maximum applicable force, but the size of such devices has limited their use in applications where high force and high-numerical-aperture (NA) microscopy must be combined. We have developed a magnetic manipulation system that is capable of applying forces in excess of 700 pN on a 1 µm paramagnetic particle and 13 nN on a 4.5 µm paramagnetic particle, forces over the full 4 sr, and a bandwidth in excess of 3 kHz while remaining compatible with a commercially available high-NA microscope objective. Our system design separates the pole tips from the flux coils so that the magnetic-field geometry at the sample is determined by removable thin-foil pole plates, allowing easy change from experiment to experiment. In addition, we have combined the magnetic manipulator with a feedback-enhanced, high-resolution (2.4 nm), high-bandwidth (10 kHz), long-range (100 µm xyz range) laser tracking system. We demonstrate the usefulness of this system in a study of the role of forces in higher-order chromosome structure and function. ©2006 American Institute of Physics

Fibrin Fibers Have Extraordinary Extensibility and Elasticity

W Liu — 2007-04-19T18:06:03-00:00

Science, Vol. 313, No. 5787. (4 August 2006), 634.

Blood clots perform an essential mechanical task, yet the mechanical behavior of fibrin fibers, which form the structural framework of a clot, is largely unknown. By using combined atomic force-fluorescence microscopy, we determined the elastic limit and extensibility of individual fibers. Fibrin fibers can be strained 180% (2.8-fold extension) without sustaining permanent lengthening, and they can be strained up to 525% (average 330%) before rupturing. This is the largest extensibility observed for protein fibers. The data imply that fibrin monomers must be able to undergo sizeable, reversible structural changes and that deformations in clots can be accommodated by individual fiber stretching. 10.1126/science.1127317

Visualization and Mechanical Manipulations of Individual Fibrin Fibers Suggest that Fiber Cross Section Has Fractal Dimension 1.3

M Guthold — 2007-04-19T18:01:12-00:00

Biophys. J., Vol. 87, No. 6. (1 December 2004), pp. 4226-4236.

We report protocols and techniques to image and mechanically manipulate individual fibrin fibers, which are key structural components of blood clots. Using atomic force microscopy-based lateral force manipulations we determined the rupture force, FR, of fibrin fibers as a function of their diameter, D, in ambient conditions. As expected, the rupture force increases with increasing diameter; however, somewhat unexpectedly, it increases as FR [~] D1.30+/-0.06. Moreover, using a combined atomic force microscopy-fluorescence microscopy instrument, we determined the light intensity, I, of single fibers, that were formed with fluorescently labeled fibrinogen, as a function of their diameter, D. Similar to the force data, we found that the light intensity, and thus the number of molecules per cross section, increases as I [~] D1.25+/-0.11. Based on these findings we propose that fibrin fibers are fractals for which the number of molecules per cross section increases as about D1.3. This implies that the molecule density varies asrho (D) [~] D-0.7, i.e., thinner fibers are denser than thicker fibers. Such a model would be consistent with the observation that fibrin fibers consist of 70-80% water and only 20-30% protein, which also suggests that fibrin fibers are very porous. 10.1529/biophysj.104.042333

Interplay of ion binding and attraction in DNA condensed by multivalent cations

Brian Todd — 2008-02-29T12:39:52-00:00

Nucl. Acids Res., Vol. 36, No. 2. (2 February 2008), pp. 501-510.

We have measured forces generated by multivalent cation-induced DNA condensation using single-molecule magnetic tweezers. In the presence of cobalt hexammine, spermidine, or spermine, stretched DNA exhibits an abrupt configurational change from extended to condensed. This occurs at a well-defined condensation force that is nearly equal to the condensation free energy per unit length. The multivalent cation concentration dependence for this condensation force gives the apparent number of multivalent cations that bind DNA upon condensation. The measurements show that the lower critical concentration for cobalt hexammine as compared to spermidine is due to a difference in ion binding, not a difference in the electrostatic energy of the condensed state as previously thought. We also show that the resolubilization of condensed DNA can be described using a traditional ManningOosawa cation adsorption model, provided that cationanion pairing at high electrolyte concentrations is taken into account. Neither overcharging nor significant alterations in the condensed state are required to describe the resolubilization of condensed DNA. The same model also describes the spermidine3+/Na+ phase diagram measured previously. 10.1093/nar/gkm1038

Opening rates of DNA hairpins: Experiment and model

Jeungphill Hanne — 2007-08-17T19:53:40-00:00

Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 1. (2007)

We present single-molecule measurements of the opening rate of DNA hairpins under mechanical tension and compare with the results obtained from a reduced-degrees-of-freedom statistical mechanics model. We extract the apparent position of the transition state s and find that the model, with no fitting parameters, reproduces the experimental measurements surprisingly well. Our values for s are different from the ones obtained in previous experiments, where, however, the experimental conditions were different (different force fields, different salt concentrations). Thus it appears that the values of s measured for relatively short hairpins are strongly affected by these experimental conditions.

Affective gaming: measuring emotion through the gamepad

Jonathan Sykes — 2007-08-02T22:30:01-00:00

(2003), pp. 732-733.

Thermodynamic Driving Force in Nucleation and Growth Processes

John Hoffman — 2007-08-09T19:10:53-00:00

The Journal of Chemical Physics, Vol. 29, No. 5. (1958), pp. 1192-1193.

Self-Assembled Water-Soluble Nucleic Acid Probe Tiles for Label-Free RNA Hybridization Assays

Yonggang Ke — 2008-01-10T23:22:09-00:00

Science, Vol. 319, No. 5860. (11 January 2008), pp. 180-183.

The DNA origami method, in which long, single-stranded DNA segments are folded into shapes by short staple segments, was used to create nucleic acid probe tiles that are molecular analogs of macroscopic DNA chips. One hundred trillion probe tiles were fabricated in one step and bear pairs of 20-nucleotide-long single-stranded DNA segments that act as probe sequences. These tiles can hybridize to their targets in solution and, after adsorption onto mica surfaces, can be examined by atomic force microscopy in order to quantify binding events, because the probe segments greatly increase in stiffness upon hybridization. The nucleic acid probe tiles have been used to study position-dependent hybridization on the nanoscale and have also been used for label-free detection of RNA. 10.1126/science.1150082

Atomic force microscope probe based controlled pushing for nanotribological characterization

M Sitti — 2008-01-15T22:32:18-00:00

Mechatronics, IEEE/ASME Transactions on, Vol. 9, No. 2. (2004), pp. 343-349.

Using an atomic force microscope (AFM) probe as a nanomanipulator, micrometer- and nanometer-sized objects, especially particles, are pushed on substrates for characterizing the object-substrate friction parameters and behavior in various environments, e.g., air, liquid, and vacuum. Two possible nanotribological characterization methods are proposed in this paper: 1) sliding the micro/nano-object on the substrate while it is attached to an AFM probe and 2) nanorobotic pushing of the micro/nano-object with the sharp tip of an AFM probe. The modeling of these methods are realized and experiments are conducted for the latter method using a piezoresistive AFM probe as a one-dimensional force sensor and nanomanipulator. In the experiments, 500-nm radius gold-coated latex particles are pushed on a silicon substrate. Preliminary results show that different frictional behavior such as sliding, rolling, and rotation could be observed, and shear stresses and frictional behavior could be estimated using these techniques at the nanoscale.

The elastohydrodynamic force on a sphere near a soft wall

J Urzay — 2007-12-18T02:18:21-00:00

Phys. Fluids, Vol. 19, No. 10. (2007)

The influence of soft boundaries on the forces experienced by a small sphere undergoing slow translation and rotation near a wall is investigated using asymptotic and numerical methods. The clearance between the sphere and the wall is assumed to be small, so that the lubrication approximation holds in the gap. The forces induced by boundary deformation break the symmetry of the Stokes equations, leading to irreversibility of the motion of the sphere and yielding a nonzero lift force. A general formulation, applicable to any constitutive equation of the wall, is presented, and an asymptotic analysis for slightly soft boundaries is developed and applied to a thin compressible elastic layer coating a rigid surface. Expressions are derived for the elastohydrodynamic lift exerted on a sphere moving parallel to the wall, which include the influence of the sphere rotation in the direction of its motion. The results extend and correct previous work, and are different from those for the elastohydrodynamic motion of a cylinder near a wall, in that the geometry eliminates the occurrence of maximum lift and optimum choice of the material properties of the boundary. © 2007 American Institute of Physics. Art. No.: 103106

Dual-trap technique for reduction of low-frequency noise in force measuring optical tweezers

Markus Klein — 2008-01-13T00:27:30-00:00

Appl. Opt., Vol. 46, No. 3. (20 January 2007), pp. 405-412.

High-resolution long-time force measurements by optical tweezers are often limited by low- frequency (1/ f ) noise. A dual-trap technique is presented that can reduce such noise in the force signal. It incorporates a second trap (a reference trap) that probes the noise in the system and it is based upon the assumption that the low-frequency parts of the noise from the two traps are correlated. A subtraction of the low-frequency signal from the reference trap from the signal from the force measuring trap will therefore yield a net signal that is significantly less influenced by noise. It is shown that this dual-trap technique can reduce the noise in the force signal up to 60% depending on detection bandwidth.

Photonic force spectroscopy on metallic and absorbing nanoparticles

Patrick Chaumet — 2007-08-12T19:37:24-00:00

Physical Review B (Condensed Matter and Materials Physics), Vol. 71, No. 4. (2005)

We present a detailed study of the optical trapping and manipulation of nanoparticles with complex permittivity using an apertureless near-field probe. We use a three-dimensional, self-consistent description of the electromagnetic scattering processes that accounts for retardation and the intricate many-body interaction between the substrate, the particle, and the probe. We analyze the influence of absorption on the optical force. For metals we describe how the optical force spectrum is influenced by the optical response of the metal, and in particular by plasmon resonances. We find that the optical force spectrum can provide an intrinsic signature of the particle composition which can be used to achieve a material-selective trapping and nanomanipulation.

Measurements of trapping efficiency and stiffness in optical tweezers

N Malagnino — 2007-08-29T04:17:59-00:00

Optics Communications, Vol. 214 (December 2002), pp. 15-24.

<A HREF="/cgi-bin/nph-data_query?link_type=EJOURNAL&bibcode=2002OptCo.214...15M">Electronic Article Available</A> from <A HREF="http://www.elsevier.com">Elsevier Science.</A>

Force measurements of optical tweezers in electro-optical cages

G Fuhr — 2007-08-29T04:14:15-00:00

Applied Physics A: Materials Science & Processing, Vol. 67 (1998), pp. 385-390.

We introduce a new device for measuring optically induced forces on microparticles and cells. It uses high-frequency electric field cages (octopoles); dielectrophoretic force calculations allow calibration of optical tweezers. A microsystem in the form of a microscope slide was fabricated by photolithography and electrically connected to a 4-phase high-frequency generator. The possibilities and advantages of a combined electro-optical trap are exemplified by the manipulation of latex beads and human erythrocytes. The system clearly detects misalignments of optical tweezers. In spite of instabilities it is possible to obtain a force-versus-power calibration. Further possibilities of the technique are discussed.

Determination of the force constant of a single-beam gradient trap by measurement of backscattered light

MEJ Friese — 2007-08-29T04:12:32-00:00

Appl. Opt., Vol. 35 (December 1996), pp. 7112-7116.

Available on OSA CDROM

DNA: A Programmable Force Sensor

C Albrecht — 2007-08-24T19:18:42-00:00

Science, Vol. 301 (July 2003), pp. 367-370.

Direct quantification of biomolecular interaction by single-molecule force spectroscopy has evolved into a powerful tool for materials and life sciences. We introduce an approach in which the unbinding forces required to break intermolecular bonds are measured in a differential format by comparison with a known reference bond (here, a short DNA duplex). In addition to a marked increase in sensitivity and force resolution, which enabled us to resolve single-base pair mismatches, this concept allows for highly specific parallel assays. This option was exploited to overcome cross-reactions of antibodies in a protein biochip application.

Characterization of Trapping Force on Metallic Mie Particles

PC Ke — 2007-08-29T03:49:29-00:00

Appl. Opt., Vol. 38 (January 1999), pp. 160-167.

Not Available

Particle manipulation with nonadiabatic ponderomotive forces

IY Dodin — 2007-08-08T22:10:03-00:00

Physics of Plasmas, Vol. 14, No. 5. (2007)

Average, or ponderomotive potentials effectively seen by particles in oscillating fields allow advanced techniques of particle manipulation inaccessible with static potentials. In strongly inhomogeneous fields the ponderomotive force is phase dependent, and the particle dynamics resembles that of a quantum object in a conservative barrier. Probabilistic transmission through a ponderomotive potential is then possible and can be used for particle beam slicing. Resonant fields can also cool and trap particles exhibiting natural oscillations (e.g., Larmor rotation), as well as transmit them asymmetrically; hence, acting as one-way walls. An approximate integral of particle motion is found for this case and a new ponderomotive potential is introduced accordingly. ©2007 American Institute of Physics

Single-Molecule Analysis by Noncontact Atomic Force Microscopy

A Sasahara — 2007-08-01T02:13:56-00:00

J. Phys. Chem. B, Vol. 105, No. 1. (11 January 2001), pp. 1-4.

Abstract: Atomic force microscopy operated in noncontact mode (NC-AFM) is a promising method for high-resolution sensing of a wide range of materials regardless of conductivity. Its feasibility in single-molecule analysis is demonstrated; formate (HCOO-) and acetate (CH3COO-) molecules were identified molecule-by-molecule on a TiO2 substrate. The character of the tip-molecule force responsible for the observed image contrast is discussed.

New calibration method for position detector for simultaneous measurements of force constants and local viscosity in optical tweezers

A Buosciolo — 2007-12-10T03:48:34-00:00

Optics Communications, Vol. 230 (February 2004), pp. 357-368.

<A HREF="/cgi-bin/nph-data_query?link_type=EJOURNAL&bibcode=2004OptCo.230..357B">Electronic Article Available</A> from <A HREF="http://www.elsevier.com">Elsevier Science.</A>

Light Traps Using Spontaneous Forces

DE Pritchard — 2008-02-05T03:04:33-00:00

Physical Review Letters, Vol. 57, No. 3. (21 July 1986), 310.

We show that the optical Earnshaw theorem does not always apply to atoms and that it is possible to confine atoms by spontaneous light forces produced by static laser beams. A necessary condition for such traps is that the atomic transition rate cannot depend only on the light intensity. We give several general approaches by which this condition can be met and present a number of specific trap designs illustrating these approaches. These traps have depths on the order of a kelvin and volumes of several cubic centimeters.

Observation of a single-beam gradient force optical trap for dielectric particles

A Ashkin — 2008-02-05T02:58:19-00:00

Opt. Lett., Vol. 11, No. 5. (1 May 1986), 288.

Neutron Reflectivity and Atomic Force Microscopy Studies of a Lipid Bilayer in Water Adsorbed to the Surface of a Silicon Single Crystal

BW Koenig — 2007-09-03T02:01:13-00:00

Langmuir, Vol. 12, No. 5. (6 March 1996), pp. 1343-1350.

Abstract: Specular reflection of neutrons has been used to characterize the structure of single lipid bilayers adsorbed to a planar silicon surface from aqueous solution. We used a novel experimental setup which significantly decreased the incoherent background scattering and allowed us to measure neutron reflectivities as low as 5 × 10-7. Thicknesses and neutron scattering length densities were determined by a fitting procedure using (i) randomly generated smooth functions represented by parametric B-splines and (ii) stepped functions based on the theoretical lipid composition. The size of lipid domains at the surface and the degree of surface coverage were determined by atomic force microscopy. Chain-protonated and -deuterated dipalmitoylphosphatidylcholine (DPPC) bilayers were investigated in 2H2O and a mixture of 2H2O and H2O which matches the scattering density of silicon. Also, one measurement on a distearoylphosphatidylcholine bilayer which has longer acyl chains was performed for comparison. The lipid adsorbs to the silicon surface as a continuous layer interrupted by irregularly shaped uncovered areas which are 100-500 Å in size. The surface coverage was estimated to be 70 ± 20%. The reflectivity measurements on DPPC at 60 C show a silicon oxide layer with a thickness of the order of 4 Å, a rough silicon oxide/water layer between silicon oxide and lipid with a thickness between 2 and 8 Å, and a single lipid bilayer. Fitting resolved a central membrane layer with a thickness of 28 ± 2 Å which represents the lipid hydrocarbon chains. This layer is sandwiched between interface membrane layers of lipid head groups and water which are 11.5 ± 1 Å in thickness. The angstrom-scale thickness changes of the central membrane layer as a function of the phase state of the lipid and of the length of the hydrocarbon chains are easily detected.

Optical Traps as Force Transducers: The Effects of Focusing the Trapping Beam through a Dielectric Interface

AC Dogariu — 2008-02-06T01:19:49-00:00

Langmuir, Vol. 16, No. 6. (21 March 2000), pp. 2770-2778.

Abstract: The use of optical forces generated by a focused laser beam for manipulating single polymer chains and colloidal particles has begun to receive increasing attention in polymer and colloid science and in biophysics. Devices based on such optical traps are increasingly used for probing the elasticity of single polymer chains and for studying the structure and mechanical behavior of biopolymers and their relation to biological activity. Colloidal forces and viscoelastic behavior of the suspending fluids can also be examined through the use of optical traps as force transducers and from the dynamics of optically bound probe particles. Such applications require a precise understanding of the trap potential and its dependence on the distance between the trap center and the glass/liquid interfaces that exist in experimental arrangements. This paper addresses some of the issues relevant to the above class of applications of optical traps using wave optics calculations. It is shown that the use of simple geometric optics corrections for the change in focus caused by a dielectric interface could lead to errors in the estimation of the measured forces. The occurrence of secondary traps and corresponding deviations from the commonly assumed harmonicity of trap potentials are also identified.

Electromagnetic force on a metallic particle in the presence of a dielectric surface

PC Chaumet — 2008-02-06T01:17:26-00:00

Physical Review B, Vol. 62, No. 16. (15 October 2000), 11185.

By using a method; previously established; to calculate electromagnetic fields; we compute the force of light upon a metallic particle. This procedure is based on both Maxwell’s stress tensor and the couple dipole method. With these tools; we study the force when the particle is over a flat dielectric surface. The multiple interaction of light between the particle and the surface is fully taken into account. The wave illuminating the particle is either evanescent or propagating depending an whether or not total internal reflection takes place. We analyze the behavior of this force on either a small or a large particle in terms of the wavelength. A remarkable result obtained for evanescent field illumination is that the force on a small silver particle can be either attractive or repulsive depending on the wavelength. This behavior also varies as the particle becomes larger.