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
Subscribe to:
Posts (Atom)