Warren Colomb, Susanta K. Sarkar
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. 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 forced-based single-molecule experiments and gaining biological insights. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques.
DOI
Friday, January 30, 2015
Optically driven oscillations of ellipsoidal particles. Part II: Ray-optics calculations
J. -C. Loudet, B. M. Mihiretie, B. Pouligny
We report numerical calculations on the mechanical effects of light on micrometer-sized dielectric ellipsoids immersed in water. We used a simple two-dimensional ray-optics model to compute the radiation pressure forces and torques exerted on the object as a function of position and orientation within the laser beam. Integration of the equations of motion, written in the Stokes limit, yields the particle dynamics that we investigated for different aspect ratios k . Whether the beam is collimated or focused, the results show that above a critical aspect ratio kC, the ellipsoids cannot be stably trapped on the beam axis; the particle never comes to rest and rather oscillates permanently in a back-and-forth motion involving both translation and rotation in the vicinity of the beam. Such oscillations are a direct evidence of the non-conservative character of optical forces. Conversely, stable trapping can be achieved for k < k C with the particle standing idle in a vertical position. These predictions are in very good qualitative agreement with experimental observations. The physical origin of the instability may be understood from the force and torque fields whose structures greatly depend on the ellipsoid aspect ratio and beam diameter. The oscillations arise from a non-linear coupling of the forces and torques and the torque amplitude was identified as the bifurcation control parameter. Interestingly, simulations predict that sustained oscillations can be suppressed through the use of two coaxial counterpropagating beams, which may be of interest whenever a static equilibrium is required as in basic force and torque measurements or technological applications.
DOI
We report numerical calculations on the mechanical effects of light on micrometer-sized dielectric ellipsoids immersed in water. We used a simple two-dimensional ray-optics model to compute the radiation pressure forces and torques exerted on the object as a function of position and orientation within the laser beam. Integration of the equations of motion, written in the Stokes limit, yields the particle dynamics that we investigated for different aspect ratios k . Whether the beam is collimated or focused, the results show that above a critical aspect ratio kC, the ellipsoids cannot be stably trapped on the beam axis; the particle never comes to rest and rather oscillates permanently in a back-and-forth motion involving both translation and rotation in the vicinity of the beam. Such oscillations are a direct evidence of the non-conservative character of optical forces. Conversely, stable trapping can be achieved for k < k C with the particle standing idle in a vertical position. These predictions are in very good qualitative agreement with experimental observations. The physical origin of the instability may be understood from the force and torque fields whose structures greatly depend on the ellipsoid aspect ratio and beam diameter. The oscillations arise from a non-linear coupling of the forces and torques and the torque amplitude was identified as the bifurcation control parameter. Interestingly, simulations predict that sustained oscillations can be suppressed through the use of two coaxial counterpropagating beams, which may be of interest whenever a static equilibrium is required as in basic force and torque measurements or technological applications.
DOI
Optically driven oscillations of ellipsoidal particles. Part I: Experimental observations
B. M. Mihiretie, P. Snabre, J. -C. Loudet, B. Pouligny
We report experimental observations of the mechanical effects of light on ellipsoidal micrometre-sized dielectric particles, in water as the continuous medium. The particles, made of polystyrene, have shapes varying between near disk-like (aspect ratio k = 0.2 to very elongated needle-like (k = 8 . Rather than the very tightly focused beam geometry of optical tweezers, we use a moderately focused laser beam to manipulate particles individually by optical levitation. The geometry allows us varying the longitudinal position of the particle, and to capture images perpendicular to the beam axis. Experiments show that moderate-k particles are radially trapped with their long axis lying parallel to the beam. Conversely, elongated (k > 3 or flattened (k < 0.3 ellipsoids never come to rest, and permanently “dance” around the beam, through coupled translation-rotation motions. The oscillations are shown to occur in general, be the particle in bulk water or close to a solid boundary, and may be periodic or irregular. We provide evidence for two bifurcations between static and oscillating states, at k ≈ 0.33 and k ≈ 3 for oblate and prolate ellipsoids, respectively. Based on a recently developed 2-dimensional ray-optics simulation (Mihiretie et al., EPL 100, 48005 (2012)), we propose a simple model that allows understanding the physical origin of the oscillations.
DOI
We report experimental observations of the mechanical effects of light on ellipsoidal micrometre-sized dielectric particles, in water as the continuous medium. The particles, made of polystyrene, have shapes varying between near disk-like (aspect ratio k = 0.2 to very elongated needle-like (k = 8 . Rather than the very tightly focused beam geometry of optical tweezers, we use a moderately focused laser beam to manipulate particles individually by optical levitation. The geometry allows us varying the longitudinal position of the particle, and to capture images perpendicular to the beam axis. Experiments show that moderate-k particles are radially trapped with their long axis lying parallel to the beam. Conversely, elongated (k > 3 or flattened (k < 0.3 ellipsoids never come to rest, and permanently “dance” around the beam, through coupled translation-rotation motions. The oscillations are shown to occur in general, be the particle in bulk water or close to a solid boundary, and may be periodic or irregular. We provide evidence for two bifurcations between static and oscillating states, at k ≈ 0.33 and k ≈ 3 for oblate and prolate ellipsoids, respectively. Based on a recently developed 2-dimensional ray-optics simulation (Mihiretie et al., EPL 100, 48005 (2012)), we propose a simple model that allows understanding the physical origin of the oscillations.
DOI
Flexible confinement leads to multiple relaxation regimes in glassy colloidal liquids
Ian Williams, Erdal C. Oğuz, Paul Bartlett, Hartmut Löwen and C. Patrick Royall
Understanding relaxation of supercooled fluids is a major challenge and confining such systems can lead to bewildering behaviour. Here, we exploit an optically confined colloidal model system in which we use reduced pressure as a control parameter. The dynamics of the system are “Arrhenius” at low and moderate pressure, but at higher pressures relaxation is faster than expected. We associate this faster relaxation with a decrease in density adjacent to the confining boundary due to local ordering in the system enabled by the flexible wall.
DOI
Understanding relaxation of supercooled fluids is a major challenge and confining such systems can lead to bewildering behaviour. Here, we exploit an optically confined colloidal model system in which we use reduced pressure as a control parameter. The dynamics of the system are “Arrhenius” at low and moderate pressure, but at higher pressures relaxation is faster than expected. We associate this faster relaxation with a decrease in density adjacent to the confining boundary due to local ordering in the system enabled by the flexible wall.
DOI
Thursday, January 29, 2015
Topology and self-assembly of defect-colloidal superstructure in confined chiral nematic liquid crystals
M. B. Pandey, P. J. Ackerman, A. Burkart, T. Porenta, S. Žumer, and Ivan I. Smalyukh
We describe formation of defect-colloidal superstructures induced by microspheres with normal surface anchoring dispersed in chiral nematic liquid crystals in confinement-unwound homeotropic cells. Using three-dimensional nonlinear optical imaging of the director field, we demonstrate that some of the induced defects have nonsingular solitonic nature while others are singular point and line topological defects. The common director structures induced by individual microspheres have dipolar symmetry. These topological dipoles are formed by the particle and a hyperbolic point defect (or small disclination loop) of elementary hedgehog charge opposite to that of a sphere with perpendicular boundary conditions, which in cells with thickness over equilibrium cholesteric pitch ratio approaching unity are additionally interspaced by a looped double-twist cylinder of continuous director deformations. The long-range elastic interactions are probed by holographic optical tweezers and videomicroscopy, providing insights to the physical underpinnings behind self-assembled colloidal structures entangled by twisted solitons. Computer-simulated field and defect configurations induced by the colloidal particles and their assemblies, which are obtained by numerically minimizing the Landau–de Gennes free energy, are in agreement with the experimental findings.
DOI
We describe formation of defect-colloidal superstructures induced by microspheres with normal surface anchoring dispersed in chiral nematic liquid crystals in confinement-unwound homeotropic cells. Using three-dimensional nonlinear optical imaging of the director field, we demonstrate that some of the induced defects have nonsingular solitonic nature while others are singular point and line topological defects. The common director structures induced by individual microspheres have dipolar symmetry. These topological dipoles are formed by the particle and a hyperbolic point defect (or small disclination loop) of elementary hedgehog charge opposite to that of a sphere with perpendicular boundary conditions, which in cells with thickness over equilibrium cholesteric pitch ratio approaching unity are additionally interspaced by a looped double-twist cylinder of continuous director deformations. The long-range elastic interactions are probed by holographic optical tweezers and videomicroscopy, providing insights to the physical underpinnings behind self-assembled colloidal structures entangled by twisted solitons. Computer-simulated field and defect configurations induced by the colloidal particles and their assemblies, which are obtained by numerically minimizing the Landau–de Gennes free energy, are in agreement with the experimental findings.
DOI
Microfluidic cell sorting: a review of the advances in the separation of cells from debulking to rare cell isolation
C. Wyatt Shields IV, Catherine D. Reyes and Gabriel P. López
Accurate and high throughput cell sorting is a critical enabling technology in molecular and cellular biology, biotechnology, and medicine. While conventional methods can provide high efficiency sorting in short timescales, advances in microfluidics have enabled the realization of miniaturized devices offering similar capabilities that exploit a variety of physical principles. We classify these technologies as either active or passive. Active systems generally use external fields (e.g., acoustic, electric, magnetic, and optical) to impose forces to displace cells for sorting, whereas passive systems use inertial forces, filters, and adhesion mechanisms to purify cell populations. Cell sorting on microchips provides numerous advantages over conventional methods by reducing the size of necessary equipment, eliminating potentially biohazardous aerosols, and simplifying the complex protocols commonly associated with cell sorting. Additionally, microchip devices are well suited for parallelization, enabling complete lab-on-a-chip devices for cellular isolation, analysis, and experimental processing. In this review, we examine the breadth of microfluidic cell sorting technologies, while focusing on those that offer the greatest potential for translation into clinical and industrial practice and that offer multiple, useful functions. We organize these sorting technologies by the type of cell preparation required (i.e., fluorescent label-based sorting, bead-based sorting, and label-free sorting) as well as by the physical principles underlying each sorting mechanism.
DOI
Accurate and high throughput cell sorting is a critical enabling technology in molecular and cellular biology, biotechnology, and medicine. While conventional methods can provide high efficiency sorting in short timescales, advances in microfluidics have enabled the realization of miniaturized devices offering similar capabilities that exploit a variety of physical principles. We classify these technologies as either active or passive. Active systems generally use external fields (e.g., acoustic, electric, magnetic, and optical) to impose forces to displace cells for sorting, whereas passive systems use inertial forces, filters, and adhesion mechanisms to purify cell populations. Cell sorting on microchips provides numerous advantages over conventional methods by reducing the size of necessary equipment, eliminating potentially biohazardous aerosols, and simplifying the complex protocols commonly associated with cell sorting. Additionally, microchip devices are well suited for parallelization, enabling complete lab-on-a-chip devices for cellular isolation, analysis, and experimental processing. In this review, we examine the breadth of microfluidic cell sorting technologies, while focusing on those that offer the greatest potential for translation into clinical and industrial practice and that offer multiple, useful functions. We organize these sorting technologies by the type of cell preparation required (i.e., fluorescent label-based sorting, bead-based sorting, and label-free sorting) as well as by the physical principles underlying each sorting mechanism.
DOI
Photochemically synthesized silver nanostructures on tapered fiber as plasmonic tweezers for surface enhanced Raman scattering applications
Jiajie Chen, Zhiwen Kang, Haifei Lu, Haixi Zhang, Wallace C.H. Choy, Nan-Kuang Chen, Ho-Pui Ho
A photochemically synthesized silver nanostructure has been fabricated on a tapered fiber. The possibility of using it for controlled trapping and releasing of target silver nanoparticles is experimentally verified. The evanescent light from fiber taper assists the synthesis of its nanostructures. After the same light source is coupled into the fiber again, the as-prepared silver nanostructure-coated tapered fiber (AgNS-TF) acts as plasmonic tweezers for trapping silver nanodecahedrons (AgNDs) with target Raman molecules immobilized on. Then we confirm the trapping event by monitoring surface enhanced Raman scattering (SERS) signals at the AgNS-TF. The proposed fiber-based scheme offers a flexible device platform for low-cost portable sensing applications.
DOI
A photochemically synthesized silver nanostructure has been fabricated on a tapered fiber. The possibility of using it for controlled trapping and releasing of target silver nanoparticles is experimentally verified. The evanescent light from fiber taper assists the synthesis of its nanostructures. After the same light source is coupled into the fiber again, the as-prepared silver nanostructure-coated tapered fiber (AgNS-TF) acts as plasmonic tweezers for trapping silver nanodecahedrons (AgNDs) with target Raman molecules immobilized on. Then we confirm the trapping event by monitoring surface enhanced Raman scattering (SERS) signals at the AgNS-TF. The proposed fiber-based scheme offers a flexible device platform for low-cost portable sensing applications.
DOI
Measurement of Lamellipodial Protrusion by Optical Trapping
Ken’ichi Sakai, Sogo Kohmoto, Daisuke Nobezawa, Sho-ichi Ikeda, and Hidetake Miyata
Lamellipodial protrusion is a fundamental step in cell locomotion. This important process is driven by actin polymerization, but its physical aspect has not yet been fully investigated. We previously studied the lamellipodial protrusion of Swiss 3T3 fibroblast cells at 33 ms temporal resolution and 10 nm accuracy by probing the motion of the cell edge with a 1 µm bead held in an optical trap. In that study, we found a transient mode of protrusion and analyzed the time variation of the protrusion velocity. In this study, we analyzed the power spectra of the fluctuations of a trap-held bead during the protrusion and found cell-specific fluctuations. The maximal amplitude of the fluctuations was 23 nm, which was estimated from the power of the fluctuations accumulated over 1.9 and 7.6 Hz. This value was significantly larger than that of the fluctuations of the trap-held bead that is not in contact with the cell edge (14 nm). The amplitude of the fluctuation of the probing bead showed a positive correlation with the cell edge velocity, suggesting that the cell-specific fluctuations play an important role in the lamellipodial protrusion.
DOI
Lamellipodial protrusion is a fundamental step in cell locomotion. This important process is driven by actin polymerization, but its physical aspect has not yet been fully investigated. We previously studied the lamellipodial protrusion of Swiss 3T3 fibroblast cells at 33 ms temporal resolution and 10 nm accuracy by probing the motion of the cell edge with a 1 µm bead held in an optical trap. In that study, we found a transient mode of protrusion and analyzed the time variation of the protrusion velocity. In this study, we analyzed the power spectra of the fluctuations of a trap-held bead during the protrusion and found cell-specific fluctuations. The maximal amplitude of the fluctuations was 23 nm, which was estimated from the power of the fluctuations accumulated over 1.9 and 7.6 Hz. This value was significantly larger than that of the fluctuations of the trap-held bead that is not in contact with the cell edge (14 nm). The amplitude of the fluctuation of the probing bead showed a positive correlation with the cell edge velocity, suggesting that the cell-specific fluctuations play an important role in the lamellipodial protrusion.
DOI
First exit times of harmonically trapped particles: a didactic review
Denis S Grebenkov
We revise the classical problem of characterizing first exit times of a harmonically trapped particle whose motion is described by a one- or multidimensional Ornstein–Uhlenbeck process. We start by recalling the main derivation steps of a propagator using Langevin and Fokker–Planck equations. The mean exit time, the moment-generating function and the survival probability are then expressed through confluent hypergeometric functions and thoroughly analyzed. We also present a rapidly converging series representation of confluent hypergeometric functions that is particularly well suited for numerical computation of eigenvalues and eigenfunctions of the governing Fokker–Planck operator. We discuss several applications of first exit times, such as the detection of time intervals during which motor proteins exert a constant force onto a tracer in optical tweezers single-particle tracking experiments; adhesion bond dissociation under mechanical stress; characterization of active periods of trend-following and mean-reverting strategies in algorithmic trading on stock markets; relation to the distribution of first crossing times of a moving boundary by Brownian motion. Some extensions are described, including diffusion under quadratic double-well potential and anomalous diffusion.
DOI
We revise the classical problem of characterizing first exit times of a harmonically trapped particle whose motion is described by a one- or multidimensional Ornstein–Uhlenbeck process. We start by recalling the main derivation steps of a propagator using Langevin and Fokker–Planck equations. The mean exit time, the moment-generating function and the survival probability are then expressed through confluent hypergeometric functions and thoroughly analyzed. We also present a rapidly converging series representation of confluent hypergeometric functions that is particularly well suited for numerical computation of eigenvalues and eigenfunctions of the governing Fokker–Planck operator. We discuss several applications of first exit times, such as the detection of time intervals during which motor proteins exert a constant force onto a tracer in optical tweezers single-particle tracking experiments; adhesion bond dissociation under mechanical stress; characterization of active periods of trend-following and mean-reverting strategies in algorithmic trading on stock markets; relation to the distribution of first crossing times of a moving boundary by Brownian motion. Some extensions are described, including diffusion under quadratic double-well potential and anomalous diffusion.
DOI
Wednesday, January 28, 2015
Sequence and Chiral Selectivity of Drug–DNA Interactions Revealed by Force Spectroscopy
Qiongzheng Hu and Prof. Shoujun Xu
Differential binding force has been used to precisely characterize the mechanical effect of a drug molecule binding to a DNA duplex. The high-resolution binding forces measured by the force-induced remnant magnetization spectroscopy (FIRMS) enable the binding behavior of drug molecules with different chirality and DNA of various sequences to be distinguished. The sequence specificity of Hg2+ and daunomycin was revealed by force spectroscopy for the first time, and the results are consistent with those obtained by other techniques. Furthermore, the two isomers of d,l-tetrahydropalmatine showed selectivity for two different DNA sequences. One particular useful feature of this approach is that the small molecules under study do not require any labels.
DOI
Differential binding force has been used to precisely characterize the mechanical effect of a drug molecule binding to a DNA duplex. The high-resolution binding forces measured by the force-induced remnant magnetization spectroscopy (FIRMS) enable the binding behavior of drug molecules with different chirality and DNA of various sequences to be distinguished. The sequence specificity of Hg2+ and daunomycin was revealed by force spectroscopy for the first time, and the results are consistent with those obtained by other techniques. Furthermore, the two isomers of d,l-tetrahydropalmatine showed selectivity for two different DNA sequences. One particular useful feature of this approach is that the small molecules under study do not require any labels.
DOI
The momentum of an electromagnetic wave inside a dielectric derived from the Snell refraction law
V.P. Torchigin, A.V. Torchigin
Author of the paper [M. Testa, Ann. Physics 336 (2013) 1] has derived a conclusion that there is a connection between the Snell refraction law and the Abraham form of the momentum of light in matter. In other words, author derived the Snell law on assumption that the momentum of light in matter decreases by n times as compared with that in free space. The conclusion is derived under assumption that the forces exerted on an optical medium by an electromagnetic field do not distinguish between polarization and free charges. We show that, on the contrary, the Minkowski form of the momentum of light in matter directly follows from the Snell law. No previous assumption is required for this purpose.
DOI
Author of the paper [M. Testa, Ann. Physics 336 (2013) 1] has derived a conclusion that there is a connection between the Snell refraction law and the Abraham form of the momentum of light in matter. In other words, author derived the Snell law on assumption that the momentum of light in matter decreases by n times as compared with that in free space. The conclusion is derived under assumption that the forces exerted on an optical medium by an electromagnetic field do not distinguish between polarization and free charges. We show that, on the contrary, the Minkowski form of the momentum of light in matter directly follows from the Snell law. No previous assumption is required for this purpose.
DOI
Laser microsurgery of cells by femtosecond laser scalpel and optical tweezers
D. S. Sitnikov, A. V. Ovchinnikov, I. V. Ilina, O. V. Chefonov, M. B. Agranat
This paper provides a brief overview of the current state of research in the field of laser microsurgery of preimplantation embryos. The combined system femtosecond laser tweezers-scalpel developed in JIHT RAS is described. A scheme of device and peculiarities of functioning its nodes as well as the ground for the choice of their parameters are presented. The results of the development of methodology for noncontact polar body biopsy of the preimplantation embryo are also presented to demonstrate the potentials of the combined multi-purpose system femtosecond laser tweezers-scalpel.
DOI
This paper provides a brief overview of the current state of research in the field of laser microsurgery of preimplantation embryos. The combined system femtosecond laser tweezers-scalpel developed in JIHT RAS is described. A scheme of device and peculiarities of functioning its nodes as well as the ground for the choice of their parameters are presented. The results of the development of methodology for noncontact polar body biopsy of the preimplantation embryo are also presented to demonstrate the potentials of the combined multi-purpose system femtosecond laser tweezers-scalpel.
DOI
Playing the notes of DNA with light: extremely high frequency nanomechanical oscillations
Abhay Kotnala, Skyler Wheaton and Reuven Gordon
We use a double nanohole (DNH) optical tweezer with two trapping lasers beating to excite the vibrational modes of single-stranded DNA (ssDNA) fragments in the extremely high frequency range. We find the resonant vibration frequency of a 20 base ssDNA to be 40 GHz. We show that the change in the resonant frequency for different lengths of the DNA strand is in good agreement with one dimensional lattice vibration theory. Thus the DNH tweezer system could distinguish between different lengths of DNA strands with resolution down to a few bases. By varying the base sequence and length, it is possible to adjust the resonance frequency vibration spectrum. The technique shows the potential for use in sequencing applications if we can improve the resolution of the present system to detect changes in resonant frequency for a single base change in a given sequence. The technique is single-molecule and label-free as compared to the existing methods used for DNA characterization like gel electrophoresis.
DOI
We use a double nanohole (DNH) optical tweezer with two trapping lasers beating to excite the vibrational modes of single-stranded DNA (ssDNA) fragments in the extremely high frequency range. We find the resonant vibration frequency of a 20 base ssDNA to be 40 GHz. We show that the change in the resonant frequency for different lengths of the DNA strand is in good agreement with one dimensional lattice vibration theory. Thus the DNH tweezer system could distinguish between different lengths of DNA strands with resolution down to a few bases. By varying the base sequence and length, it is possible to adjust the resonance frequency vibration spectrum. The technique shows the potential for use in sequencing applications if we can improve the resolution of the present system to detect changes in resonant frequency for a single base change in a given sequence. The technique is single-molecule and label-free as compared to the existing methods used for DNA characterization like gel electrophoresis.
DOI
Sunday, January 25, 2015
Force fluctuations in three-dimensional suspended fibroblasts
Florian Schlosser, Florian Rehfeldt, Christoph F. Schmidt
Cells are sensitive to mechanical cues from their environment and at the same time generate and transmit forces to their surroundings. To test quantitatively forces generated by cells not attached to a substrate, we used a dual optical trap to suspend 3T3 fibroblasts between two fibronectin-coated beads. In this simple geometry, we measured both the cells' elastic properties and the force fluctuations they generate with high bandwidth. Cell stiffness decreased substantially with both myosin inhibition by blebbistatin and serum-starvation, but not with microtubule depolymerization by nocodazole. We show that cortical forces generated by non-muscle myosin II deform the cell from its rounded shape in the frequency regime from 0.1 to 10 Hz. The amplitudes of these forces were strongly reduced by blebbistatin and serum starvation, but were unaffected by depolymerization of microtubules. Force fluctuations show a spectrum that is characteristic for an elastic network activated by random sustained stresses with abrupt transitions.
DOI
Cells are sensitive to mechanical cues from their environment and at the same time generate and transmit forces to their surroundings. To test quantitatively forces generated by cells not attached to a substrate, we used a dual optical trap to suspend 3T3 fibroblasts between two fibronectin-coated beads. In this simple geometry, we measured both the cells' elastic properties and the force fluctuations they generate with high bandwidth. Cell stiffness decreased substantially with both myosin inhibition by blebbistatin and serum-starvation, but not with microtubule depolymerization by nocodazole. We show that cortical forces generated by non-muscle myosin II deform the cell from its rounded shape in the frequency regime from 0.1 to 10 Hz. The amplitudes of these forces were strongly reduced by blebbistatin and serum starvation, but were unaffected by depolymerization of microtubules. Force fluctuations show a spectrum that is characteristic for an elastic network activated by random sustained stresses with abrupt transitions.
DOI
Helical buckling of actin inside filopodia generates traction
Natascha Leijnse, Lene B. Oddershede, and Poul M. Bendix
Cells can interact with their surroundings via filopodia, which are membrane protrusions that extend beyond the cell body. Filopodia are essential during dynamic cellular processes like motility, invasion, and cell–cell communication. Filopodia contain cross-linked actin filaments, attached to the surrounding cell membrane via protein linkers such as integrins. These actin filaments are thought to play a pivotal role in force transduction, bending, and rotation. We investigated whether, and how, actin within filopodia is responsible for filopodia dynamics by conducting simultaneous force spectroscopy and confocal imaging of F-actin in membrane protrusions. The actin shaft was observed to periodically undergo helical coiling and rotational motion, which occurred simultaneously with retrograde movement of actin inside the filopodium. The cells were found to retract beads attached to the filopodial tip, and retraction was found to correlate with rotation and coiling of the actin shaft. These results suggest a previously unidentified mechanism by which a cell can use rotation of the filopodial actin shaft to induce coiling and hence axial shortening of the filopodial actin bundle.
DOI
Cells can interact with their surroundings via filopodia, which are membrane protrusions that extend beyond the cell body. Filopodia are essential during dynamic cellular processes like motility, invasion, and cell–cell communication. Filopodia contain cross-linked actin filaments, attached to the surrounding cell membrane via protein linkers such as integrins. These actin filaments are thought to play a pivotal role in force transduction, bending, and rotation. We investigated whether, and how, actin within filopodia is responsible for filopodia dynamics by conducting simultaneous force spectroscopy and confocal imaging of F-actin in membrane protrusions. The actin shaft was observed to periodically undergo helical coiling and rotational motion, which occurred simultaneously with retrograde movement of actin inside the filopodium. The cells were found to retract beads attached to the filopodial tip, and retraction was found to correlate with rotation and coiling of the actin shaft. These results suggest a previously unidentified mechanism by which a cell can use rotation of the filopodial actin shaft to induce coiling and hence axial shortening of the filopodial actin bundle.
DOI
Actio et reactio in optical binding
Sergey Sukhov, Alexander Shalin, David Haefner, and Aristide Dogariu
The symmetry in action and reaction between interacting particulate matter breaks down when the interaction is mediated by an out-of-equilibrium environment. Nevertheless, even in this case, the space translational invariance still imposes the conservation of canonical momentum. Here we show that optical binding of an asymmetric material system can result in non-reciprocal interactions between constituents. We demonstrate that a non-conservative force applies to the center of mass of an optically bound dimer of dissimilar particles, which leads to an unexpected action in the transversal direction. The sign and the magnitude of this positional force depend on the abrupt phase transitions in the properties of the asymmetric dimer.
DOI
The symmetry in action and reaction between interacting particulate matter breaks down when the interaction is mediated by an out-of-equilibrium environment. Nevertheless, even in this case, the space translational invariance still imposes the conservation of canonical momentum. Here we show that optical binding of an asymmetric material system can result in non-reciprocal interactions between constituents. We demonstrate that a non-conservative force applies to the center of mass of an optically bound dimer of dissimilar particles, which leads to an unexpected action in the transversal direction. The sign and the magnitude of this positional force depend on the abrupt phase transitions in the properties of the asymmetric dimer.
DOI
Formation of contour optical traps using a four-channel liquid crystal focusing device
A V Korobtsov, S P Kotova, N N Losevsky, A M Mayorova and S A Samagin
The capabilities and specific features of the formation and dynamic control of so-called contour optical traps using a fourchannel liquid crystal modulator are studied theoretically and experimentally. Circular, elliptical and C-shaped traps are formed. Trapping and confinement of absorbing micro-objects by the formed traps are demonstrated.
DOI
The capabilities and specific features of the formation and dynamic control of so-called contour optical traps using a fourchannel liquid crystal modulator are studied theoretically and experimentally. Circular, elliptical and C-shaped traps are formed. Trapping and confinement of absorbing micro-objects by the formed traps are demonstrated.
DOI
Wednesday, January 14, 2015
Strong THz and Infrared Optical Forces on a Suspended Single-Layer Graphene Sheet
S. Hossein Mousavi, Peter T. Rakich, and Zheng Wang
Single-layer graphene exhibits exceptional mechanical properties attractive for optomechanics: it combines low mass density, large tensile modulus, and low bending stiffness. However, at visible wavelengths, graphene absorbs weakly and reflects even less, thereby is inadequate to generate large optical forces needed in optomechanics. Here, we numerically show that a single-layer graphene sheet is sufficient to produce strong optical forces under terahertz or infrared illumination. For a system as simple as graphene suspended atop a uniform substrate, high reflectivity from the substrate is crucial in creating a standing-wave pattern, leading to a strong optical force on graphene. This force is readily tunable in amplitude and direction by adjusting the suspension height. In particular, repellent optical forces can levitate graphene to a series of stable equilibrium heights above the substrate. One of the key parameters to maximize the optical force is the excitation frequency: peak forces are found near the scattering frequency of free carriers in graphene. With a dynamically controllable Fermi level, graphene opens up new possibilities of tunable nanoscale optomechanical devices.
DOI
Single-layer graphene exhibits exceptional mechanical properties attractive for optomechanics: it combines low mass density, large tensile modulus, and low bending stiffness. However, at visible wavelengths, graphene absorbs weakly and reflects even less, thereby is inadequate to generate large optical forces needed in optomechanics. Here, we numerically show that a single-layer graphene sheet is sufficient to produce strong optical forces under terahertz or infrared illumination. For a system as simple as graphene suspended atop a uniform substrate, high reflectivity from the substrate is crucial in creating a standing-wave pattern, leading to a strong optical force on graphene. This force is readily tunable in amplitude and direction by adjusting the suspension height. In particular, repellent optical forces can levitate graphene to a series of stable equilibrium heights above the substrate. One of the key parameters to maximize the optical force is the excitation frequency: peak forces are found near the scattering frequency of free carriers in graphene. With a dynamically controllable Fermi level, graphene opens up new possibilities of tunable nanoscale optomechanical devices.
DOI
Optical spanner based on the transfer of spin angular momentum of light in semiconductors
Houquan Liu
An optical spanner is a light beam that can exert a torque on a microscopic object. When a circularly polarized beam irradiates semiconductors, the output light becomes partially circularly polarized. Thus the total angular momentum of the light beam is changed, which leads to a torque, creating an optical spanner on the semiconductor. In this letter, we investigate this kind of optical spanner in detail, and its electric and magnetic control are discussed.
DOI
An optical spanner is a light beam that can exert a torque on a microscopic object. When a circularly polarized beam irradiates semiconductors, the output light becomes partially circularly polarized. Thus the total angular momentum of the light beam is changed, which leads to a torque, creating an optical spanner on the semiconductor. In this letter, we investigate this kind of optical spanner in detail, and its electric and magnetic control are discussed.
DOI
Measurement of the Position-Dependent Electrophoretic Force on DNA in a Glass Nanocapillary
Roman D. Bulushev, Lorenz J. Steinbock, Sergey Khlybov, Julian F. Steinbock, Ulrich F. Keyser, and Aleksandra Radenovic
The electrophoretic force on a single DNA molecule inside a glass nanocapillary depends on the opening size and varies with the distance along the symmetrical axis of the nanocapillary. Using optical tweezers and DNA-coated beads, we measured the stalling forces and mapped the position-dependent force profiles acting on DNA inside nanocapillaries of different sizes. We showed that the stalling force is higher in nanocapillaries of smaller diameters. The position-dependent force profiles strongly depend on the size of the nanocapillary opening, and for openings smaller than 20 nm, the profiles resemble the behavior observed in solid-state nanopores. To characterize the position-dependent force profiles in nanocapillaries of different sizes, we used a model that combines information from both analytical approximations and numerical calculations.
DOI
The electrophoretic force on a single DNA molecule inside a glass nanocapillary depends on the opening size and varies with the distance along the symmetrical axis of the nanocapillary. Using optical tweezers and DNA-coated beads, we measured the stalling forces and mapped the position-dependent force profiles acting on DNA inside nanocapillaries of different sizes. We showed that the stalling force is higher in nanocapillaries of smaller diameters. The position-dependent force profiles strongly depend on the size of the nanocapillary opening, and for openings smaller than 20 nm, the profiles resemble the behavior observed in solid-state nanopores. To characterize the position-dependent force profiles in nanocapillaries of different sizes, we used a model that combines information from both analytical approximations and numerical calculations.
DOI
Sunday, January 11, 2015
Accounting for inertia effects to access the high-frequency microrheology of viscoelastic fluids
P. Domínguez-García, Frédéric Cardinaux, Elena Bertseva, László Forró, Frank Scheffold, and Sylvia Jeney
We study the Brownian motion of microbeads immersed in water and in a viscoelastic wormlike micelles solution by optical trapping interferometry and diffusing wave spectroscopy. Through the mean-square displacement obtained from both techniques, we deduce the mechanical properties of the fluids at high frequencies by explicitly accounting for inertia effects of the particle and the surrounding fluid at short time scales. For wormlike micelle solutions, we recover the 3/4 scaling exponent for the loss modulus over two decades in frequency as predicted by the theory for semiflexible polymers.
DOI
We study the Brownian motion of microbeads immersed in water and in a viscoelastic wormlike micelles solution by optical trapping interferometry and diffusing wave spectroscopy. Through the mean-square displacement obtained from both techniques, we deduce the mechanical properties of the fluids at high frequencies by explicitly accounting for inertia effects of the particle and the surrounding fluid at short time scales. For wormlike micelle solutions, we recover the 3/4 scaling exponent for the loss modulus over two decades in frequency as predicted by the theory for semiflexible polymers.
DOI
Dynamics of self-organized aggregation of resonant nanoparticles in a laser field
V. V. Slabko, A. S. Tsipotan, A. S. Aleksandrovsky, E. A. Slyusareva
Self-organized aggregation of nanoparticles in external resonant laser field is considered using Brownian dynamics model. Formation probabilities are calculated for the pair of particles in dependence on laser wavelength and mutual orientation of particles. Times required for aggregation are calculated. Possibility of efficient aggregation using pulsed laser is deduced.
DOI
Self-organized aggregation of nanoparticles in external resonant laser field is considered using Brownian dynamics model. Formation probabilities are calculated for the pair of particles in dependence on laser wavelength and mutual orientation of particles. Times required for aggregation are calculated. Possibility of efficient aggregation using pulsed laser is deduced.
DOI
Trigger loop folding determines transcription rate of Escherichia coli’s RNA polymerase
Yara X. Mejia, Evgeny Nudler, and Carlos Bustamante
Two components of the RNA polymerase (RNAP) catalytic center, the bridge helix and the trigger loop (TL), have been linked with changes in elongation rate and pausing. Here, single molecule experiments with the WT and two TL-tip mutants of the Escherichia coli enzyme reveal that tip mutations modulate RNAP’s pause-free velocity, identifying TL conformational changes as one of two rate-determining steps in elongation. Consistent with this observation, we find a direct correlation between helix propensity of the modified amino acid and pause-free velocity. Moreover, nucleotide analogs affect transcription rate, suggesting that their binding energy also influences TL folding. A kinetic model in which elongation occurs in two steps, TL folding on nucleoside triphosphate (NTP) binding followed by NTP incorporation/pyrophosphate release, quantitatively accounts for these results. The TL plays no role in pause recovery remaining unfolded during a pause. This model suggests a finely tuned mechanism that balances transcription speed and fidelity.
DOI
Two components of the RNA polymerase (RNAP) catalytic center, the bridge helix and the trigger loop (TL), have been linked with changes in elongation rate and pausing. Here, single molecule experiments with the WT and two TL-tip mutants of the Escherichia coli enzyme reveal that tip mutations modulate RNAP’s pause-free velocity, identifying TL conformational changes as one of two rate-determining steps in elongation. Consistent with this observation, we find a direct correlation between helix propensity of the modified amino acid and pause-free velocity. Moreover, nucleotide analogs affect transcription rate, suggesting that their binding energy also influences TL folding. A kinetic model in which elongation occurs in two steps, TL folding on nucleoside triphosphate (NTP) binding followed by NTP incorporation/pyrophosphate release, quantitatively accounts for these results. The TL plays no role in pause recovery remaining unfolded during a pause. This model suggests a finely tuned mechanism that balances transcription speed and fidelity.
DOI
Saturday, January 10, 2015
Light-controlled topological charge in a nematic liquid crystal
Maryam Nikkhou, Miha Škarabot, Simon Čopar, Miha Ravnik, Slobodan Žumer & Igor Muševič
Creating, imaging, and transforming the topological charge in a superconductor, a superfluid, a system of cold atoms, or a soft ferromagnet is a difficult—if not impossible—task because of the shortness of the length scales and lack of control. The length scale and softness of defects in liquid crystals allow the easy observation of charges, but it is difficult to control charge creation. Here we demonstrate full control over the creation, manipulation and analysis of topological charges that are pinned to a microfibre in a nematic liquid crystal. Oppositely charged pairs are created through the Kibble–Zurek mechanism by applying a laser-induced local temperature quench in the presence of symmetry-breaking boundaries. The pairs are long-lived, oppositely charged rings or points that either attract and annihilate, or form a long-lived, charge-neutral loop made of two segments with a fractional topological charge.
DOI
Creating, imaging, and transforming the topological charge in a superconductor, a superfluid, a system of cold atoms, or a soft ferromagnet is a difficult—if not impossible—task because of the shortness of the length scales and lack of control. The length scale and softness of defects in liquid crystals allow the easy observation of charges, but it is difficult to control charge creation. Here we demonstrate full control over the creation, manipulation and analysis of topological charges that are pinned to a microfibre in a nematic liquid crystal. Oppositely charged pairs are created through the Kibble–Zurek mechanism by applying a laser-induced local temperature quench in the presence of symmetry-breaking boundaries. The pairs are long-lived, oppositely charged rings or points that either attract and annihilate, or form a long-lived, charge-neutral loop made of two segments with a fractional topological charge.
DOI
Reversible Control of the Equilibrium Size of a Single Aerosol Droplet by Change in Relative Humidity
Shoji ISHIZAKA, Kunihiro YAMAUCHI, Noboru KITAMURA
Noncontact levitation of single micrometer-sized water droplets in air can be achieved by a laser trapping technique. The equilibrium size of a water droplet is quite sensitive to relative humidity in the surrounding gas phase. In order to investigate the physical and chemical properties of single water droplets in air as a function of the droplet size or solute concentration, laser trapping experiments were conducted under controlled humidity conditions. In this study, we developed a trapping chamber equipped with a relative humidity controller and demonstrated the reversible control of the equilibrium size of a single droplet levitated in air through a change in relative humidity. Furthermore, relative humidity was successfully evaluated by means of cavity enhanced Raman spectroscopy of a trapped water droplet.
DOI
Noncontact levitation of single micrometer-sized water droplets in air can be achieved by a laser trapping technique. The equilibrium size of a water droplet is quite sensitive to relative humidity in the surrounding gas phase. In order to investigate the physical and chemical properties of single water droplets in air as a function of the droplet size or solute concentration, laser trapping experiments were conducted under controlled humidity conditions. In this study, we developed a trapping chamber equipped with a relative humidity controller and demonstrated the reversible control of the equilibrium size of a single droplet levitated in air through a change in relative humidity. Furthermore, relative humidity was successfully evaluated by means of cavity enhanced Raman spectroscopy of a trapped water droplet.
DOI
A microscopic steam engine implemented in an optical tweezer
Pedro A. Quinto-Su
The introduction of improved steam engines at the end of the 18th century marked the start of the industrial revolution and the birth of classical thermodynamics. Currently, there is great interest in miniaturizing heat engines, but so far traditional heat engines operating with the expansion and compression of gas have not reached length scales shorter than one millimeter. Here, a micrometer-sized piston steam engine is implemented in an optical tweezer. The piston is a single colloidal microparticle that is driven by explosive vapourization of the surrounding liquid (cavitation bubbles) and by optical forces at a rate between a few tens of Hertz and one kilo-Hertz. The operation of the engine allows to exert impulsive forces with optical tweezers and induce streaming in the liquid, similar to the effect of transducers when driven at acoustic and ultrasound frequencies.
DOI
The introduction of improved steam engines at the end of the 18th century marked the start of the industrial revolution and the birth of classical thermodynamics. Currently, there is great interest in miniaturizing heat engines, but so far traditional heat engines operating with the expansion and compression of gas have not reached length scales shorter than one millimeter. Here, a micrometer-sized piston steam engine is implemented in an optical tweezer. The piston is a single colloidal microparticle that is driven by explosive vapourization of the surrounding liquid (cavitation bubbles) and by optical forces at a rate between a few tens of Hertz and one kilo-Hertz. The operation of the engine allows to exert impulsive forces with optical tweezers and induce streaming in the liquid, similar to the effect of transducers when driven at acoustic and ultrasound frequencies.
DOI
Field Enhancement and Gradient Force in the Graphene-Coated Nanowire Pairs
Bofeng Zhu, Guobin Ren, Yang Yang, Yixiao Gao, Beilei Wu, Yudong Lian, Jing Wang, Shuisheng Jian
We investigate the field enhancement and gradient force in the graphene-coated nanowire pairs in this paper. The real part of modal index, normalized propagation lengths, surface charge distributions and field distributions of the six lowest orders’ plasmon modes in the graphene-coated nanowire pairs is presented. Studies have shown that the six lowest orders’ modes can be divided into two groups due to the monopole-monopole hybridizations or the dipole-dipole interactions. The field enhancement in the slot region of the graphene-coated nanowire pairs can be as large as 107 times, which is six orders’ magnitude larger than the counterpart in silver nanowire pairs. Meanwhile, gradient force between the two nanowires can be as high as 20 nN·μm−1·mW−1, which is more than one order of magnitude (∼50 times) larger than the silver nanowire pairs and the previous results from other slot waveguides or coupled waveguides. The field enhancement or gradient force in the graphene-coated nanowire pairs may have applications in single biomolecule manipulation or detection.
DOI
We investigate the field enhancement and gradient force in the graphene-coated nanowire pairs in this paper. The real part of modal index, normalized propagation lengths, surface charge distributions and field distributions of the six lowest orders’ plasmon modes in the graphene-coated nanowire pairs is presented. Studies have shown that the six lowest orders’ modes can be divided into two groups due to the monopole-monopole hybridizations or the dipole-dipole interactions. The field enhancement in the slot region of the graphene-coated nanowire pairs can be as large as 107 times, which is six orders’ magnitude larger than the counterpart in silver nanowire pairs. Meanwhile, gradient force between the two nanowires can be as high as 20 nN·μm−1·mW−1, which is more than one order of magnitude (∼50 times) larger than the silver nanowire pairs and the previous results from other slot waveguides or coupled waveguides. The field enhancement or gradient force in the graphene-coated nanowire pairs may have applications in single biomolecule manipulation or detection.
DOI
Multiple optical trapping based on high-order axially symmetric polarized beams
Zhou Zhe-Hai, Zhu Lian-Qing
Multiple optical trapping with high-order axially symmetric polarized beams (ASPBs) is studied theoretically, and a scheme based on far-field optical trapping with ASPBs is first proposed. The focused fields and the corresponding gradient forces on Rayleigh dielectric particles are calculated for the scheme. The calculated results indicate that multiple ultra-small focused spots can be achieved, and multiple nanometer-sized particles with refractive index higher than the ambient can be trapped simultaneously near these focused spots, which are expected to enhance the capabilities of traditional optical trapping systems and provide a solution for massive multiple optical trapping of nanometer-sized particles.
DOI
Multiple optical trapping with high-order axially symmetric polarized beams (ASPBs) is studied theoretically, and a scheme based on far-field optical trapping with ASPBs is first proposed. The focused fields and the corresponding gradient forces on Rayleigh dielectric particles are calculated for the scheme. The calculated results indicate that multiple ultra-small focused spots can be achieved, and multiple nanometer-sized particles with refractive index higher than the ambient can be trapped simultaneously near these focused spots, which are expected to enhance the capabilities of traditional optical trapping systems and provide a solution for massive multiple optical trapping of nanometer-sized particles.
DOI
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