Juan Carlos Cordova, Dana N. Reinemann, Daniel J. Laky, William R. Hesse, Sophie K. Tushak, Zane L. Weltman, Kelsea B. Best, Rizia Bardhan, Matthew J. Lang
Due to their high spatial resolution and precise application of force, optical traps are widely used to study the mechanics of biomolecules and biopolymers at the single-molecule level. Recently, core–shell particles with optical properties that enhance their trapping ability represent promising candidates for high-force experiments. To fully harness their properties, methods for functionalizing these particles with biocompatible handles are required. Here, a straightforward synthesis is provided for producing functional titania core–shell microparticles with proteins and nucleic acids by adding a silane–thiol chemical group to the shell surface. These particles display higher trap stiffness compared to conventional plastic beads featured in optical tweezers experiments. These core–shell microparticles are also utilized in biophysical assays such as amyloid fiber pulling and actin rupturing to demonstrate their high-force applications. It is anticipated that the functionalized core–shells can be used to probe the mechanics of stable proteins structures that are inaccessible using current trapping techniques.
DOI
Friday, February 16, 2018
Influence on the saturable absorption of the induced losses by photodeposition of zinc nanoparticles in an optical fiber
L. C. Gómez-Pavón, G. J. Lozano-Perera, A. Luis-Ramos, J. M. Muñoz-Pacheco, J. P. Padilla-Martínez, and P. Zaca-Morán
In this work, the influence of induced losses on the saturable absorption by zinc nanoparticles photodeposited onto the core of an optical fiber end is reported. Samples with different losses were obtained by the photodeposition technique using a continuous wave laser at 1550 nm. The nonlinear absorption of the saturable absorber was characterized by the P-scan technique using a high-gain pulsed erbium-doped fiber amplifier. The results have demonstrated that for optical fibers with variable induced losses by deposited nanoparticles, the modulation depth increases proportionally based on the nonlinear absorption coefficient. With induced losses fixed at 3 dB, it was demonstrated that the modulation depth increased as a function of the optical power used in the photodeposition process. The saturation intensity of the saturable absorber presents small shifts for higher intensities.
DOI
In this work, the influence of induced losses on the saturable absorption by zinc nanoparticles photodeposited onto the core of an optical fiber end is reported. Samples with different losses were obtained by the photodeposition technique using a continuous wave laser at 1550 nm. The nonlinear absorption of the saturable absorber was characterized by the P-scan technique using a high-gain pulsed erbium-doped fiber amplifier. The results have demonstrated that for optical fibers with variable induced losses by deposited nanoparticles, the modulation depth increases proportionally based on the nonlinear absorption coefficient. With induced losses fixed at 3 dB, it was demonstrated that the modulation depth increased as a function of the optical power used in the photodeposition process. The saturation intensity of the saturable absorber presents small shifts for higher intensities.
DOI
Self-Organization of Metal Nanoparticles in Light: Electrodynamics–Molecular Dynamics Simulations and Optical Binding Experiments
Patrick McCormack, Fei Han, and Zijie Yan
Light-driven self-organization of metal nanoparticles (NPs) can lead to unique optical matter systems, yet simulation of such self-organization (i.e., optical binding) is a complex computational problem that increases nonlinearly with system size. Here we show that a combined electrodynamics–molecular dynamics simulation technique can simulate the trajectories and predict stable configurations of silver NPs in optical fields. The simulated dynamic equilibrium of a two-NP system matches the probability density of oscillations for two optically bound NPs obtained experimentally. The predicted stable configurations for up to eight NPs are further compared to experimental observations of silver NP clusters formed by optical binding in a Bessel beam. All configurations are confirmed to form in real systems, including pentagonal clusters with five-fold symmetry. Our combined simulations and experiments have revealed a diverse optical matter system formed by anisotropic optical binding interactions, providing a new strategy to discover artificial materials.
DOI
Light-driven self-organization of metal nanoparticles (NPs) can lead to unique optical matter systems, yet simulation of such self-organization (i.e., optical binding) is a complex computational problem that increases nonlinearly with system size. Here we show that a combined electrodynamics–molecular dynamics simulation technique can simulate the trajectories and predict stable configurations of silver NPs in optical fields. The simulated dynamic equilibrium of a two-NP system matches the probability density of oscillations for two optically bound NPs obtained experimentally. The predicted stable configurations for up to eight NPs are further compared to experimental observations of silver NP clusters formed by optical binding in a Bessel beam. All configurations are confirmed to form in real systems, including pentagonal clusters with five-fold symmetry. Our combined simulations and experiments have revealed a diverse optical matter system formed by anisotropic optical binding interactions, providing a new strategy to discover artificial materials.
DOI
Interactions of single nanoparticles in nematic liquid crystal
M. Škarabot, A. V. Ryzhkova, I. Muševič
We studied interactions of single silica nanoparticles with homeotropic surface anchoring in a confined planar nematic liquid crystal cell. Nanoparticles form stable pairs down to a size of 35 nm with the pair binding energy proportional to the size of the particle. 22 nm particles do not form stable pairs, only metastable states were observed due to strong thermal motion and electrostatic repulsion. These nanoparticles strongly interact with the confining surfaces and the larger clusters, which prevents the formation of stable homogenous dispersions. In addition we have shown that nanoparticles are strongly attracted by topological defects induced by the microparticles. The origin of the attractive forces in nanoparticle dispersions is the minimization of free energy. These forces strongly depend on the strength and type of the liquid crystal anchoring at the surface of the nanoparticles.
DOI
We studied interactions of single silica nanoparticles with homeotropic surface anchoring in a confined planar nematic liquid crystal cell. Nanoparticles form stable pairs down to a size of 35 nm with the pair binding energy proportional to the size of the particle. 22 nm particles do not form stable pairs, only metastable states were observed due to strong thermal motion and electrostatic repulsion. These nanoparticles strongly interact with the confining surfaces and the larger clusters, which prevents the formation of stable homogenous dispersions. In addition we have shown that nanoparticles are strongly attracted by topological defects induced by the microparticles. The origin of the attractive forces in nanoparticle dispersions is the minimization of free energy. These forces strongly depend on the strength and type of the liquid crystal anchoring at the surface of the nanoparticles.
DOI
Immersion and Contact Efflorescence Induced by Mineral Dust Particles
Shuichi B. Ushijima, Ryan D. Davis, and Margaret A. Tolbert
The phase state of inorganic salt aerosols impacts their properties, including the ability to undergo hygroscopic growth, catalyze heterogeneous reactions, and act as cloud condensation nuclei. Here, we report the first observation of contact efflorescence by mineral dust aerosol. The efflorescence of aqueous ammonium sulfate ((NH4)2SO4) and sodium chloride (NaCl) droplets by contact with three types of mineral dust particles (illite, montmorillonite, and NX illite), were examined using an optical levitation chamber. Immersion mode efflorescence was also studied for comparison. We find that in the presence of mineral dust particles, crystallization occurred at a higher relative humidity (RH) when compared to the homogeneous phase transition. Additionally, crystallization by contact mode efflorescence occurred at a higher RH than the corresponding immersion mode. Crystallization efficiencies in the contact mode exhibited an ion-specific trend consistent with the Hoffmeister series. Estimates for lifetimes of a salt droplet to collide with dust particles suggests that collisions between the two aerosol types are likely to occur before the salt aerosol is removed by other atmospheric processes. Such collisions could then lead to the crystallization of salt droplets that would otherwise have remained liquid, changing the overall impact that salt aerosols have on atmospheric chemistry and climate.
DOI
The phase state of inorganic salt aerosols impacts their properties, including the ability to undergo hygroscopic growth, catalyze heterogeneous reactions, and act as cloud condensation nuclei. Here, we report the first observation of contact efflorescence by mineral dust aerosol. The efflorescence of aqueous ammonium sulfate ((NH4)2SO4) and sodium chloride (NaCl) droplets by contact with three types of mineral dust particles (illite, montmorillonite, and NX illite), were examined using an optical levitation chamber. Immersion mode efflorescence was also studied for comparison. We find that in the presence of mineral dust particles, crystallization occurred at a higher relative humidity (RH) when compared to the homogeneous phase transition. Additionally, crystallization by contact mode efflorescence occurred at a higher RH than the corresponding immersion mode. Crystallization efficiencies in the contact mode exhibited an ion-specific trend consistent with the Hoffmeister series. Estimates for lifetimes of a salt droplet to collide with dust particles suggests that collisions between the two aerosol types are likely to occur before the salt aerosol is removed by other atmospheric processes. Such collisions could then lead to the crystallization of salt droplets that would otherwise have remained liquid, changing the overall impact that salt aerosols have on atmospheric chemistry and climate.
DOI
Statics and dynamics of DNA knotting
Enzo Orlandini
Knots and entanglement in polymers and biopolymers such as DNA and proteins constitute a timely topic that spans various scientific disciplines ranging from physics to chemistry, biology and mathematics. Although in the past many advancements have been made in understanding the equilibrium knotting probability and knot complexity of long polymer chains in solutions, many questions have been addressed in recent years by both experimental and theoretical means—for instance, how the knotting probability depends on the quality of the solvent, the elastic properties of the molecule and its degree of confinement. How knots form, evolve and eventually disappear in a fluctuating chain. Are the equilibrium and non-equilibrium properties of knotted molecules affected by the knot swelling/shrinking dynamics? Moreover, thanks to the great advance in nanotechnology and micromanipulation techniques, nowadays knots can be 'manually' tied in a single DNA molecule, followed during their motion along the chains, forced to pass through nanopores, or stretched by external forces or elongational flows. All these experimental approaches allow access to new information on the interplay of topology and polymer physics, and this has opened new perspectives in the field. Here, we provide an overview of the current knowledge of this topic, stressing the main results obtained, including the recent developments in experimental and computational approaches. Since almost all experiments on knotting involve DNA, the review will be mainly focused on the topological properties of this fascinating and biologically relevant molecule.
DOI
Knots and entanglement in polymers and biopolymers such as DNA and proteins constitute a timely topic that spans various scientific disciplines ranging from physics to chemistry, biology and mathematics. Although in the past many advancements have been made in understanding the equilibrium knotting probability and knot complexity of long polymer chains in solutions, many questions have been addressed in recent years by both experimental and theoretical means—for instance, how the knotting probability depends on the quality of the solvent, the elastic properties of the molecule and its degree of confinement. How knots form, evolve and eventually disappear in a fluctuating chain. Are the equilibrium and non-equilibrium properties of knotted molecules affected by the knot swelling/shrinking dynamics? Moreover, thanks to the great advance in nanotechnology and micromanipulation techniques, nowadays knots can be 'manually' tied in a single DNA molecule, followed during their motion along the chains, forced to pass through nanopores, or stretched by external forces or elongational flows. All these experimental approaches allow access to new information on the interplay of topology and polymer physics, and this has opened new perspectives in the field. Here, we provide an overview of the current knowledge of this topic, stressing the main results obtained, including the recent developments in experimental and computational approaches. Since almost all experiments on knotting involve DNA, the review will be mainly focused on the topological properties of this fascinating and biologically relevant molecule.
DOI
Thursday, February 15, 2018
Single charging events on colloidal particles in a nonpolar liquid with surfactant
Caspar Schreuer, Stijn Vandewiele, Toon Brans, Filip Strubbe, Kristiaan Neyts, and Filip Beunis
Electrical charging of colloidal particles in nonpolar liquids due to surfactant additives is investigated intensively, motivated by its importance in a variety of applications. Most methods rely on average electrophoretic mobility measurements of many particles, which provide only indirect information on the charging mechanism. In the present work, we present a method that allows us to obtain direct information on the charging mechanism, by measuring the charge fluctuations on individual particles with a precision higher than the elementary charge using optical trapping electrophoresis. We demonstrate the capabilities of the method by studying the influence of added surfactant OLOA 11000 on the charging of single colloidal PMMA particles in dodecane. The particle charge and the frequency of charging events are investigated both below and above the critical micelle concentration (CMC) and with or without applying a DC offset voltage. It is found that at least two separate charging mechanisms are present below the critical micelle concentration. One mechanism is a process where the particle is stripped from negatively charged ionic molecules. An increase in the charging frequency with increased surfactant concentration suggests a second mechanism that involves single surfactant molecules. Above the CMC, neutral inverse micelles can also be involved in the charging process.
DOI
Electrical charging of colloidal particles in nonpolar liquids due to surfactant additives is investigated intensively, motivated by its importance in a variety of applications. Most methods rely on average electrophoretic mobility measurements of many particles, which provide only indirect information on the charging mechanism. In the present work, we present a method that allows us to obtain direct information on the charging mechanism, by measuring the charge fluctuations on individual particles with a precision higher than the elementary charge using optical trapping electrophoresis. We demonstrate the capabilities of the method by studying the influence of added surfactant OLOA 11000 on the charging of single colloidal PMMA particles in dodecane. The particle charge and the frequency of charging events are investigated both below and above the critical micelle concentration (CMC) and with or without applying a DC offset voltage. It is found that at least two separate charging mechanisms are present below the critical micelle concentration. One mechanism is a process where the particle is stripped from negatively charged ionic molecules. An increase in the charging frequency with increased surfactant concentration suggests a second mechanism that involves single surfactant molecules. Above the CMC, neutral inverse micelles can also be involved in the charging process.
DOI
The mechano-chemistry of a monomeric reverse transcriptase
Omri Malik, Hadeel Khamis, Sergei Rudnizky, Ariel Kaplan
Retroviral reverse transcriptase catalyses the synthesis of an integration-competent dsDNA molecule, using as a substrate the viral RNA. Using optical tweezers, we follow the Murine Leukemia Virus reverse transcriptase as it performs strand-displacement polymerization on a template under mechanical force. Our results indicate that reverse transcriptase functions as a Brownian ratchet, with dNTP binding as the rectifying reaction of the ratchet. We also found that reverse transcriptase is a relatively passive enzyme, able to polymerize on structured templates by exploiting their thermal breathing. Finally, our results indicate that the enzyme enters the recently characterized backtracking state from the pre-translocation complex.
DOI
Retroviral reverse transcriptase catalyses the synthesis of an integration-competent dsDNA molecule, using as a substrate the viral RNA. Using optical tweezers, we follow the Murine Leukemia Virus reverse transcriptase as it performs strand-displacement polymerization on a template under mechanical force. Our results indicate that reverse transcriptase functions as a Brownian ratchet, with dNTP binding as the rectifying reaction of the ratchet. We also found that reverse transcriptase is a relatively passive enzyme, able to polymerize on structured templates by exploiting their thermal breathing. Finally, our results indicate that the enzyme enters the recently characterized backtracking state from the pre-translocation complex.
DOI
An Accurate Perception Method for Low Contrast Bright Field Microscopy in Heterogeneous Microenvironments
Keshav Rajasekaran, Ekta Samani, Manasa Bollavaram, John Stewart and Ashis G. Banerjee
Automated optical tweezers-based robotic manipulation of microscale objects requires real-time visual perception for estimating the states, i.e., positions and orientations, of the objects. Such visual perception is particularly challenging in heterogeneous environments comprising mixtures of biological and colloidal objects, such as cells and microspheres, when the popular imaging modality of low contrast bright field microscopy is used. In this paper, we present an accurate method to address this challenge. Our method combines many well-established image processing techniques such as blob detection, histogram equalization, erosion, and dilation with a convolutional neural network in a novel manner. We demonstrate the effectiveness of our processing pipeline in perceiving objects of both regular and irregular shapes in heterogeneous microenvironments of varying compositions. The neural network, in particular, helps in distinguishing the individual microspheres present in dense clusters.
DOI
Automated optical tweezers-based robotic manipulation of microscale objects requires real-time visual perception for estimating the states, i.e., positions and orientations, of the objects. Such visual perception is particularly challenging in heterogeneous environments comprising mixtures of biological and colloidal objects, such as cells and microspheres, when the popular imaging modality of low contrast bright field microscopy is used. In this paper, we present an accurate method to address this challenge. Our method combines many well-established image processing techniques such as blob detection, histogram equalization, erosion, and dilation with a convolutional neural network in a novel manner. We demonstrate the effectiveness of our processing pipeline in perceiving objects of both regular and irregular shapes in heterogeneous microenvironments of varying compositions. The neural network, in particular, helps in distinguishing the individual microspheres present in dense clusters.
DOI
Lossless Brownian Information Engine
Govind Paneru, Dong Yun Lee, Tsvi Tlusty, and Hyuk Kyu Pak
We report on a lossless information engine that converts nearly all available information from an error-free feedback protocol into mechanical work. Combining high-precision detection at a resolution of 1 nm with ultrafast feedback control, the engine is tuned to extract the maximum work from information on the position of a Brownian particle. We show that the work produced by the engine achieves a bound set by a generalized second law of thermodynamics, demonstrating for the first time the sharpness of this bound. We validate a generalized Jarzynski equality for error-free feedback-controlled information engines.
DOI
We report on a lossless information engine that converts nearly all available information from an error-free feedback protocol into mechanical work. Combining high-precision detection at a resolution of 1 nm with ultrafast feedback control, the engine is tuned to extract the maximum work from information on the position of a Brownian particle. We show that the work produced by the engine achieves a bound set by a generalized second law of thermodynamics, demonstrating for the first time the sharpness of this bound. We validate a generalized Jarzynski equality for error-free feedback-controlled information engines.
DOI
Plasmonic waveguide design for the enhanced forward stimulated brillouin scattering in diamond
Qiang Liu, Luigi Bibbó, Sacharia Albin, Qiong Wang, Mi Lin, Huihui Lu & Zhengbiao Ouyang
We propose a scheme of metal/dielectric/metal waveguide for the enhanced forward stimulated Brillouin scattering (FSBS) in diamond that is mediated by gap surface plasmons. Numerical results based on finite-element method show that the maximum Brillouin gain in the small gap (~100 nm) can exceed 106 W−1 m−1, which is three orders of magnitude higher than that in diamond-only waveguides. It is found that the radiation pressure that exists at the boundaries of metal and diamond plays a dominant role in contributing to the enhanced forward stimulated Brillouin gain, although electrostrictive forces interfere destructively. Detailed study shows that high FSBS gain can still be obtained regardless of the photoelastic property of the dielectric material in the proposed plasmonic waveguide. The strong photon-phonon coupling in this gap-surface-plasmon waveguide may make our design useful in the development of phonon laser, RF wave generation and optomechanical information processing in quantum system.
DOI
We propose a scheme of metal/dielectric/metal waveguide for the enhanced forward stimulated Brillouin scattering (FSBS) in diamond that is mediated by gap surface plasmons. Numerical results based on finite-element method show that the maximum Brillouin gain in the small gap (~100 nm) can exceed 106 W−1 m−1, which is three orders of magnitude higher than that in diamond-only waveguides. It is found that the radiation pressure that exists at the boundaries of metal and diamond plays a dominant role in contributing to the enhanced forward stimulated Brillouin gain, although electrostrictive forces interfere destructively. Detailed study shows that high FSBS gain can still be obtained regardless of the photoelastic property of the dielectric material in the proposed plasmonic waveguide. The strong photon-phonon coupling in this gap-surface-plasmon waveguide may make our design useful in the development of phonon laser, RF wave generation and optomechanical information processing in quantum system.
DOI
Electric field induced charging of colloidal particles in a nonpolar liquid
Caspar Schreuer, Stijn Vandewiele, Filip Strubbe, Kristiaan Neyts, Filip Beunis
Colloidal particles in a pure nonpolar solvent are expected to be in a state of dynamic equilibrium where a particle’s charge fluctuates around a stable mean value. However, we find that PHSA-coated PMMA microparticles in dodecane gain positive charge over time. We hypothesize that this phenomenon is prompted by the high electric field (∼1 V/µm) that is applied in these measurements. Hence, we expect the reaction rate at which charge builds up on the particle to change when modifying the measurement parameters.
Single elementary charging and discharging events can be resolved by measuring the charge of PHSA-coated PMMA particles with optical trapping electrophoresis. With this technique, the influence of the electric field amplitude and frequency, particle size, electrode material and acquired charge can be investigated.
The rate of the charging phenomenon is proportional to the amplitude of the applied electric field and the charging stops when the voltage is switched off. We propose a reaction mechanism where the particle sheds negatively charged ions. This mechanism can account for all the experimental observations of the electric field induced charging phenomenon.
DOI
Colloidal particles in a pure nonpolar solvent are expected to be in a state of dynamic equilibrium where a particle’s charge fluctuates around a stable mean value. However, we find that PHSA-coated PMMA microparticles in dodecane gain positive charge over time. We hypothesize that this phenomenon is prompted by the high electric field (∼1 V/µm) that is applied in these measurements. Hence, we expect the reaction rate at which charge builds up on the particle to change when modifying the measurement parameters.
Single elementary charging and discharging events can be resolved by measuring the charge of PHSA-coated PMMA particles with optical trapping electrophoresis. With this technique, the influence of the electric field amplitude and frequency, particle size, electrode material and acquired charge can be investigated.
The rate of the charging phenomenon is proportional to the amplitude of the applied electric field and the charging stops when the voltage is switched off. We propose a reaction mechanism where the particle sheds negatively charged ions. This mechanism can account for all the experimental observations of the electric field induced charging phenomenon.
DOI
Dynamics of a colloidal particle near a thermoosmotic wall under illumination
Xin Lou, Nan Yu, Rui Liu, Ke Chen and Mingcheng Yang
The effects of light on colloidal particles in solution are multiple, including transfer of photonic linear/angular momentum and heating of the particles or their surroundings. The temperature increase around colloidal particles due to light heating can drive a thermoosmotic flow along a nearby boundary wall, which significantly influences the motion of the particles. Here we perform mesoscopic dynamics simulations to study two typical scenarios, where thermoosmosis is critical. In the first scenario, we consider a light-absorbing colloidal particle heated by uniform illumination. Depending on the fluid–wall interactions, the thermoosmotic flow generated by the wall can exert a long-ranged hydrodynamic attraction or repulsion on the “hot” Brownian particle, which leads to a strong accumulation/depletion of the particle to/from the boundary. In the second scenario, we investigate the motion of a colloidal particle confined by an optical tweezer in a light-absorbing solution. In this case, thermoosmosis can induce a unidirectional rotation of the trapped particle, whose direction is determined by thermoosmotic properties of the wall. We show that colloidal particles near a thermoosmotic wall exhibit rich dynamics. Our results can be applied for the manipulation of colloidal particles in microfluidics.
DOI
The effects of light on colloidal particles in solution are multiple, including transfer of photonic linear/angular momentum and heating of the particles or their surroundings. The temperature increase around colloidal particles due to light heating can drive a thermoosmotic flow along a nearby boundary wall, which significantly influences the motion of the particles. Here we perform mesoscopic dynamics simulations to study two typical scenarios, where thermoosmosis is critical. In the first scenario, we consider a light-absorbing colloidal particle heated by uniform illumination. Depending on the fluid–wall interactions, the thermoosmotic flow generated by the wall can exert a long-ranged hydrodynamic attraction or repulsion on the “hot” Brownian particle, which leads to a strong accumulation/depletion of the particle to/from the boundary. In the second scenario, we investigate the motion of a colloidal particle confined by an optical tweezer in a light-absorbing solution. In this case, thermoosmosis can induce a unidirectional rotation of the trapped particle, whose direction is determined by thermoosmotic properties of the wall. We show that colloidal particles near a thermoosmotic wall exhibit rich dynamics. Our results can be applied for the manipulation of colloidal particles in microfluidics.
DOI
Wednesday, February 14, 2018
Femtosecond Laser Printing of Single Ge and SiGe Nanoparticles with Electric and Magnetic Optical Resonances
Denis M. Zhigunov, Andrey B. Evlyukhin, Alexander S. Shalin, Urs Zywietz, and Boris N. Chichkov
A recently introduced femtosecond laser printing technique was further developed for the fabrication of crystalline single Ge and SiGe nanoparticles (NPs). Amorphous Ge and SiGe thin films deposited by e-beam evaporation on a transparent substrate were used as donors. The developed approach is based on a laser-induced forward transfer process, which provides an opportunity for NP-controlled positioning on different types of receiver substrates. The size of the generated nanoparticles can be varied from about 100 to 300 nm depending on the laser pulse energy and wavelength. The crystallinity and composition of nanoparticles are both confirmed by the Raman spectroscopy measurements. The experimental visible scattering spectra of single nanoparticles are found to be well coincident with theoretical simulations performed on the basis of Mie theory. It is demonstrated that Ge and SiGe nanoparticles are characterized by electric and magnetic dipole resonances in the visible and near-infrared spectral ranges, which is promising for photonic applications.
DOI
A recently introduced femtosecond laser printing technique was further developed for the fabrication of crystalline single Ge and SiGe nanoparticles (NPs). Amorphous Ge and SiGe thin films deposited by e-beam evaporation on a transparent substrate were used as donors. The developed approach is based on a laser-induced forward transfer process, which provides an opportunity for NP-controlled positioning on different types of receiver substrates. The size of the generated nanoparticles can be varied from about 100 to 300 nm depending on the laser pulse energy and wavelength. The crystallinity and composition of nanoparticles are both confirmed by the Raman spectroscopy measurements. The experimental visible scattering spectra of single nanoparticles are found to be well coincident with theoretical simulations performed on the basis of Mie theory. It is demonstrated that Ge and SiGe nanoparticles are characterized by electric and magnetic dipole resonances in the visible and near-infrared spectral ranges, which is promising for photonic applications.
DOI
Overstretching partially alkyne functionalized dsDNA using near infrared optical tweezers
Allan Raudsepp, Lisa M. Kent, Simon B. Hall, Martin A. K. Williams
The force-extension behaviour of synthesized double-stranded DNAs (dsDNAs) designed to have 2.1% or 6.6% of the thymine bases alkyne functionalized was studied using near infrared (NIR) optical tweezers. Measurements were carried out on substrates with and without flurophores covalently attached to the alkyne moiety over an extended force range ( pN) and results were compared to those obtained from an unmodified control. In accordance with earlier work [1] (measured over a force range pN), the force-extension of the dsDNA containing 2.1% modified-bases agreed well with that of the control. By contrast, the force-extension of the dsDNA containing 6.6% modified-bases showed an increasing deviation from that of the control as the dsDNA extension approached the molecule's contour length. These results indicate that incorporating alkyne functionalized bases can modify the mechanical properties of the dsDNA and that degree of functionalization should be carefully considered if a fluorescent mechanical analogue is required. A discrepancy between 1) the control dsDNA force-extension measured in Ref. [1] and that measured here and 2) dsDNA extensions carried out on the same duplex at different laser powers was noted; this was attributed to beam heating by the NIR trapping laser which was estimated to raise the local temperature at the optical traps by .
DOI
The force-extension behaviour of synthesized double-stranded DNAs (dsDNAs) designed to have 2.1% or 6.6% of the thymine bases alkyne functionalized was studied using near infrared (NIR) optical tweezers. Measurements were carried out on substrates with and without flurophores covalently attached to the alkyne moiety over an extended force range ( pN) and results were compared to those obtained from an unmodified control. In accordance with earlier work [1] (measured over a force range pN), the force-extension of the dsDNA containing 2.1% modified-bases agreed well with that of the control. By contrast, the force-extension of the dsDNA containing 6.6% modified-bases showed an increasing deviation from that of the control as the dsDNA extension approached the molecule's contour length. These results indicate that incorporating alkyne functionalized bases can modify the mechanical properties of the dsDNA and that degree of functionalization should be carefully considered if a fluorescent mechanical analogue is required. A discrepancy between 1) the control dsDNA force-extension measured in Ref. [1] and that measured here and 2) dsDNA extensions carried out on the same duplex at different laser powers was noted; this was attributed to beam heating by the NIR trapping laser which was estimated to raise the local temperature at the optical traps by .
DOI
All-optical manipulation of micrometer-sized metallic particles
Yuquan Zhang, Xiujie Dou, Yanmeng Dai, Xianyou Wang, Changjun Min, and Xiaocong Yuan
Optical traps use focused laser beams to generate forces on targeted objects ranging in size from nanometers to micrometers. However, for their high coefficients of scattering and absorption, micrometer-sized metallic particles were deemed non-trappable in three dimensions using a single beam. This barrier is now removed. We demonstrate, both in theory and experiment, three-dimensional (3D) dynamic all-optical manipulations of micrometer-sized gold particles under high focusing conditions. The force of gravity is found to balance the positive axial optical force exerted on particles in an inverted optical tweezers system to form two trapping positions along the vertical direction. Both theoretical and experimental results confirm that stable 3D manipulations are achievable for these particles regardless of beam polarization and wavelength. The present work opens up new opportunities for a variety of in-depth research requiring metallic particles.
DOI
Optical traps use focused laser beams to generate forces on targeted objects ranging in size from nanometers to micrometers. However, for their high coefficients of scattering and absorption, micrometer-sized metallic particles were deemed non-trappable in three dimensions using a single beam. This barrier is now removed. We demonstrate, both in theory and experiment, three-dimensional (3D) dynamic all-optical manipulations of micrometer-sized gold particles under high focusing conditions. The force of gravity is found to balance the positive axial optical force exerted on particles in an inverted optical tweezers system to form two trapping positions along the vertical direction. Both theoretical and experimental results confirm that stable 3D manipulations are achievable for these particles regardless of beam polarization and wavelength. The present work opens up new opportunities for a variety of in-depth research requiring metallic particles.
DOI
Real-time identification of the singleness of a trapped bead in optical tweezers
Chunguang Hu, Chenguang Su, Zelin Yun, Sirong Wang, Chengzhi He, Xiaoqing Gao, Shuai Li, Hongbin Li, Xiaodong Hu, and Xiaotang Hu
Beads trapped in optical tweezers are aligned along the optical propagation direction, which makes it difficult to determine the number of beads with bright-field microscopy. This problem also dramatically influences the measurement of the optical trapping based single-molecule force spectroscopy. Here, we propose a video processing approach to count the number of trapped micro-objects in real time. The approach uses a normalized cross-correlation algorithm and image enhancement techniques to amplify a slight change of the image induced by the entry of an exotic object. As tested, this method introduces a ∼10% change per bead to the image similarity, and up to four beads, one-by-one falling into the trap, are identified. Moreover, the feasibility of the above analysis in a moving trap is investigated. A movement of the trap leads to a fluctuation of less than 2% for the similarity signal and can be ignored in most cases. The experimental results prove that image similarity measurement is a sensitive way to monitor the interruption, which is very useful, especially during experiments. In addition, the approach is easy to apply to an existing optical tweezers system.
DOI
Beads trapped in optical tweezers are aligned along the optical propagation direction, which makes it difficult to determine the number of beads with bright-field microscopy. This problem also dramatically influences the measurement of the optical trapping based single-molecule force spectroscopy. Here, we propose a video processing approach to count the number of trapped micro-objects in real time. The approach uses a normalized cross-correlation algorithm and image enhancement techniques to amplify a slight change of the image induced by the entry of an exotic object. As tested, this method introduces a ∼10% change per bead to the image similarity, and up to four beads, one-by-one falling into the trap, are identified. Moreover, the feasibility of the above analysis in a moving trap is investigated. A movement of the trap leads to a fluctuation of less than 2% for the similarity signal and can be ignored in most cases. The experimental results prove that image similarity measurement is a sensitive way to monitor the interruption, which is very useful, especially during experiments. In addition, the approach is easy to apply to an existing optical tweezers system.
DOI
Nanoparticle–Cell Interaction: A Cell Mechanics Perspective
Dedy Septiadi, Federica Crippa, Thomas Lee Moore, Barbara Rothen-Rutishauser, Alke Petri-Fink
Progress in the field of nanoparticles has enabled the rapid development of multiple products and technologies; however, some nanoparticles can pose both a threat to the environment and human health. To enable their safe implementation, a comprehensive knowledge of nanoparticles and their biological interactions is needed. In vitro and in vivo toxicity tests have been considered the gold standard to evaluate nanoparticle safety, but it is becoming necessary to understand the impact of nanosystems on cell mechanics. Here, the interaction between particles and cells, from the point of view of cell mechanics (i.e., bionanomechanics), is highlighted and put in perspective. Specifically, the ability of intracellular and extracellular nanoparticles to impair cell adhesion, cytoskeletal organization, stiffness, and migration are discussed. Furthermore, the development of cutting-edge, nanotechnology-driven tools based on the use of particles allowing the determination of cell mechanics is emphasized. These include traction force microscopy, colloidal probe atomic force microscopy, optical tweezers, magnetic manipulation, and particle tracking microrheology.
DOI
Progress in the field of nanoparticles has enabled the rapid development of multiple products and technologies; however, some nanoparticles can pose both a threat to the environment and human health. To enable their safe implementation, a comprehensive knowledge of nanoparticles and their biological interactions is needed. In vitro and in vivo toxicity tests have been considered the gold standard to evaluate nanoparticle safety, but it is becoming necessary to understand the impact of nanosystems on cell mechanics. Here, the interaction between particles and cells, from the point of view of cell mechanics (i.e., bionanomechanics), is highlighted and put in perspective. Specifically, the ability of intracellular and extracellular nanoparticles to impair cell adhesion, cytoskeletal organization, stiffness, and migration are discussed. Furthermore, the development of cutting-edge, nanotechnology-driven tools based on the use of particles allowing the determination of cell mechanics is emphasized. These include traction force microscopy, colloidal probe atomic force microscopy, optical tweezers, magnetic manipulation, and particle tracking microrheology.
DOI
Micro-optics for microfluidic analytical applications
Hui Yang and Martin A. M. Gijs
This critical review summarizes the developments in the integration of micro-optical elements with microfluidic platforms for facilitating detection and automation of bio-analytical applications. Micro-optical elements, made by a variety of microfabrication techniques, advantageously contribute to the performance of an analytical system, especially when the latter has microfluidic features. Indeed the easy integration of optical control and detection modules with microfluidic technology helps to bridge the gap between the macroscopic world and chip-based analysis, paving the way for automated and high-throughput applications. In our review, we start the discussion with an introduction of microfluidic systems and micro-optical components, as well as aspects of their integration. We continue with a detailed description of different microfluidic and micro-optics technologies and their applications, with an emphasis on the realization of optical waveguides and microlenses. The review continues with specific sections highlighting the advantages of integrated micro-optical components in microfluidic systems for tackling a variety of analytical problems, like cytometry, nucleic acid and protein detection, cell biology, and chemical analysis applications.
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This critical review summarizes the developments in the integration of micro-optical elements with microfluidic platforms for facilitating detection and automation of bio-analytical applications. Micro-optical elements, made by a variety of microfabrication techniques, advantageously contribute to the performance of an analytical system, especially when the latter has microfluidic features. Indeed the easy integration of optical control and detection modules with microfluidic technology helps to bridge the gap between the macroscopic world and chip-based analysis, paving the way for automated and high-throughput applications. In our review, we start the discussion with an introduction of microfluidic systems and micro-optical components, as well as aspects of their integration. We continue with a detailed description of different microfluidic and micro-optics technologies and their applications, with an emphasis on the realization of optical waveguides and microlenses. The review continues with specific sections highlighting the advantages of integrated micro-optical components in microfluidic systems for tackling a variety of analytical problems, like cytometry, nucleic acid and protein detection, cell biology, and chemical analysis applications.
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Nano-opto-electro-mechanical systems
Leonardo Midolo, Albert Schliesser & Andrea Fiore
A new class of hybrid systems that couple optical, electrical and mechanical degrees of freedom in nanoscale devices is under development in laboratories worldwide. These nano-opto-electro-mechanical systems (NOEMS) offer unprecedented opportunities to control the flow of light in nanophotonic structures, at high speed and low power consumption. Drawing on conceptual and technological advances from the field of optomechanics, they also bear the potential for highly efficient, low-noise transducers between microwave and optical signals, in both the classical and the quantum domains. This Perspective discusses the fundamental physical limits of NOEMS, reviews the recent progress in their implementation and suggests potential avenues for further developments in this field.
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A new class of hybrid systems that couple optical, electrical and mechanical degrees of freedom in nanoscale devices is under development in laboratories worldwide. These nano-opto-electro-mechanical systems (NOEMS) offer unprecedented opportunities to control the flow of light in nanophotonic structures, at high speed and low power consumption. Drawing on conceptual and technological advances from the field of optomechanics, they also bear the potential for highly efficient, low-noise transducers between microwave and optical signals, in both the classical and the quantum domains. This Perspective discusses the fundamental physical limits of NOEMS, reviews the recent progress in their implementation and suggests potential avenues for further developments in this field.
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Tuesday, February 13, 2018
Optical Pulling and Pushing Forces in Bilayer P T -Symmetric Structures
Rasoul Alaee, Johan Christensen, and Muamer Kadic
We investigate the optical force exerted on a parity-time-symmetric bilayer made of balanced gain and loss. We show that an asymmetric optical pulling or pushing force can be exerted on this system depending on the direction of impinging light. The optical pulling or pushing force has a direct physical link to the optical characteristics embedded in the non-Hermitian bilayer. Furthermore, we suggest taking advantage of the optically generated asymmetric force to launch vibrations of an arbitrary shape, which is useful for the contactless probing of mechanical deformations.
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We investigate the optical force exerted on a parity-time-symmetric bilayer made of balanced gain and loss. We show that an asymmetric optical pulling or pushing force can be exerted on this system depending on the direction of impinging light. The optical pulling or pushing force has a direct physical link to the optical characteristics embedded in the non-Hermitian bilayer. Furthermore, we suggest taking advantage of the optically generated asymmetric force to launch vibrations of an arbitrary shape, which is useful for the contactless probing of mechanical deformations.
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Alternate analytic formulation of optical force on a dielectric sphere in the ray optics limit
Anita Devi and Arijit K. De
In the past, the optical force on a micrometer-sized dielectric sphere in a single-beam gradient laser trap was formulated by considering 2D distribution of rays for a plane-wave excitation. However, laser beams usually have a Gaussian transverse intensity profile, which, upon tight focusing, leads to a 3D optical trap. Here, we systematically formulate a generalized ray/geometric optics formalism for estimating force (and potential) for both flat-top and Gaussian laser beams using 2D distribution of light rays as well as 3D distribution of light cones. We also compare our method with the exact Mie theory. In addition, we present a detailed discussion on the nature of force (and potential) considering the optical Kerr effect under high-repetition-rate ultrafast pulsed excitation.
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In the past, the optical force on a micrometer-sized dielectric sphere in a single-beam gradient laser trap was formulated by considering 2D distribution of rays for a plane-wave excitation. However, laser beams usually have a Gaussian transverse intensity profile, which, upon tight focusing, leads to a 3D optical trap. Here, we systematically formulate a generalized ray/geometric optics formalism for estimating force (and potential) for both flat-top and Gaussian laser beams using 2D distribution of light rays as well as 3D distribution of light cones. We also compare our method with the exact Mie theory. In addition, we present a detailed discussion on the nature of force (and potential) considering the optical Kerr effect under high-repetition-rate ultrafast pulsed excitation.
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Label-free Imaging and Bending Analysis of Microtubules by ROCS Microscopy and Optical Trapping
Matthias D.Koch, Alexander Rohrbach
Mechanical manipulation of single cytoskeleton filaments and their monitoring over long times is difficult because of fluorescence bleaching or phototoxic protein degradation. The integration of label-free microscopy techniques, capable of imaging freely diffusing, weak scatterers such as microtubules (MTs) in real-time, and independent of their orientation, with optical trapping and tracking systems, would allow many new applications. Here, we show that rotating-coherent-scattering microscopy (ROCS) in dark-field mode can also provide strong contrast for structures far from the coverslip such as arrangements of isolated MTs and networks. We could acquire thousands of images over up to 30 min without loss in image contrast or visible photodamage. We further demonstrate the combination of ROCS imaging with fast and nanometer-precise 3D interferometric back-focal-plane tracking of multiple beads in time-shared optical traps using acoustooptic deflectors to specifically construct and microrheologically probe small microtubule networks with well-defined geometries. Thereby, we explore the frequency-dependent elastic response of single microtubule filaments between 0.5 Hz and 5 kHz, which allows for investigating their viscoelastic response up to the fourth-order bending mode. Our spectral analysis reveals constant filament stiffness at low frequencies and frequency-dependent stiffening following a power law ∼ωp with a length-dependent exponent p(L). We find further evidence for the dependence of the MT persistence length on the contour length L, which is still controversially debated. We could also demonstrate slower stiffening at high frequencies for longer filaments, which we believe is determined by the molecular architecture of the MT. Our results shed new light on the nanomechanics of this essential, multifunctional cytoskeletal element and pose new questions about the adaptability of the cytoskeleton.
DOI
Mechanical manipulation of single cytoskeleton filaments and their monitoring over long times is difficult because of fluorescence bleaching or phototoxic protein degradation. The integration of label-free microscopy techniques, capable of imaging freely diffusing, weak scatterers such as microtubules (MTs) in real-time, and independent of their orientation, with optical trapping and tracking systems, would allow many new applications. Here, we show that rotating-coherent-scattering microscopy (ROCS) in dark-field mode can also provide strong contrast for structures far from the coverslip such as arrangements of isolated MTs and networks. We could acquire thousands of images over up to 30 min without loss in image contrast or visible photodamage. We further demonstrate the combination of ROCS imaging with fast and nanometer-precise 3D interferometric back-focal-plane tracking of multiple beads in time-shared optical traps using acoustooptic deflectors to specifically construct and microrheologically probe small microtubule networks with well-defined geometries. Thereby, we explore the frequency-dependent elastic response of single microtubule filaments between 0.5 Hz and 5 kHz, which allows for investigating their viscoelastic response up to the fourth-order bending mode. Our spectral analysis reveals constant filament stiffness at low frequencies and frequency-dependent stiffening following a power law ∼ωp with a length-dependent exponent p(L). We find further evidence for the dependence of the MT persistence length on the contour length L, which is still controversially debated. We could also demonstrate slower stiffening at high frequencies for longer filaments, which we believe is determined by the molecular architecture of the MT. Our results shed new light on the nanomechanics of this essential, multifunctional cytoskeletal element and pose new questions about the adaptability of the cytoskeleton.
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Mobile nanotweezers for active colloidal manipulation
Souvik Ghosh and Ambarish Ghosh
An important goal in nanotechnology is to control and manipulate submicrometer objects in fluidic environments, for which optical traps based on strongly localized electromagnetic fields around plasmonic nanostructures can provide a promising solution. Conventional plasmonics based trapping occurs at predefined spots on the surface of a nanopatterned substrate and is severely speed-limited by the diffusion of colloidal objects into the trapping volume. As we demonstrate, these limitations can be overcome by integrating plasmonic nanostructures with magnetically driven helical microrobots and maneuvering the resultant mobile nanotweezers (MNTs) under optical illumination. These nanotweezers can be remotely maneuvered within the bulk fluid and temporarily stamped onto the microfluidic chamber surface. The working range of these MNTs matches that of state-of-the-art plasmonic tweezers and allows selective pickup, transport, release, and positioning of submicrometer objects with great speed and accuracy. The MNTs can be used in standard microfluidic chambers to manipulate one or many nano-objects in three dimensions and are applicable to a variety of materials, including bacteria and fluorescent nanodiamonds. MNTs may allow previously unknown capabilities in optical nanomanipulation by combining the strengths of two recent advances in nanotechnology.
DOI
An important goal in nanotechnology is to control and manipulate submicrometer objects in fluidic environments, for which optical traps based on strongly localized electromagnetic fields around plasmonic nanostructures can provide a promising solution. Conventional plasmonics based trapping occurs at predefined spots on the surface of a nanopatterned substrate and is severely speed-limited by the diffusion of colloidal objects into the trapping volume. As we demonstrate, these limitations can be overcome by integrating plasmonic nanostructures with magnetically driven helical microrobots and maneuvering the resultant mobile nanotweezers (MNTs) under optical illumination. These nanotweezers can be remotely maneuvered within the bulk fluid and temporarily stamped onto the microfluidic chamber surface. The working range of these MNTs matches that of state-of-the-art plasmonic tweezers and allows selective pickup, transport, release, and positioning of submicrometer objects with great speed and accuracy. The MNTs can be used in standard microfluidic chambers to manipulate one or many nano-objects in three dimensions and are applicable to a variety of materials, including bacteria and fluorescent nanodiamonds. MNTs may allow previously unknown capabilities in optical nanomanipulation by combining the strengths of two recent advances in nanotechnology.
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‘Photonic Hook’ based optomechanical nanoparticle manipulator
Angeleene S. Ang, Alina Karabchevsky, Igor V. Minin, Oleg V. Minin, Sergey V. Sukhov & Alexander S. Shalin
Specialized electromagnetic fields can be used for nanoparticle manipulation along a specific path, allowing enhanced transport and control over the particle’s motion. In this paper, we investigate the optical forces produced by a curved photonic jet, otherwise known as the “photonic hook”, created using an asymmetric cuboid. In our case, this cuboid is formed by appending a triangular prism to one side of a cube. A gold nanoparticle immersed in the cuboid’s transmitted field moves in a curved trajectory. This result could be used for moving nanoparticles around obstacles; hence we also consider the changes in the photonic hook’s forces when relatively large glass and gold obstacles are introduced at the region where the curved photonic jet is created. We show, that despite the obstacles, perturbing the field distribution, a particle can move around glass obstacles of a certain thickness. For larger glass slabs, the particle will be trapped stably near it. Moreover, we noticed that a partial obstruction of the photonic jet’s field using the gold obstacle results in a complete disruption of the particle’s trajectory.
DOI
Specialized electromagnetic fields can be used for nanoparticle manipulation along a specific path, allowing enhanced transport and control over the particle’s motion. In this paper, we investigate the optical forces produced by a curved photonic jet, otherwise known as the “photonic hook”, created using an asymmetric cuboid. In our case, this cuboid is formed by appending a triangular prism to one side of a cube. A gold nanoparticle immersed in the cuboid’s transmitted field moves in a curved trajectory. This result could be used for moving nanoparticles around obstacles; hence we also consider the changes in the photonic hook’s forces when relatively large glass and gold obstacles are introduced at the region where the curved photonic jet is created. We show, that despite the obstacles, perturbing the field distribution, a particle can move around glass obstacles of a certain thickness. For larger glass slabs, the particle will be trapped stably near it. Moreover, we noticed that a partial obstruction of the photonic jet’s field using the gold obstacle results in a complete disruption of the particle’s trajectory.
DOI
Optical forces of focused femtosecond laser pulses on nonlinear optical Rayleigh particles
Liping Gong, Bing Gu, Guanghao Rui, Yiping Cui, Zhuqing Zhu, and Qiwen Zhan
The principle of optical trapping is conventionally based on the interaction of optical fields with linear-induced polarizations. However, the optical force originating from the nonlinear polarization becomes significant when nonlinear optical nanoparticles are trapped by femtosecond laser pulses. Herein we develop the time-averaged optical forces on a nonlinear optical nanoparticle using high-repetition-rate femtosecond laser pulses, based on the linear and nonlinear polarization effects. We investigate the dependence of the optical forces on the magnitudes and signs of the refractive nonlinearities. It is found that the self-focusing effect enhances the trapping ability, whereas the self-defocusing effect leads to the splitting of the potential well at the focal plane and destabilizes the optical trap. Our results show good agreement with the reported experimental observations and provide theoretical support for capturing nonlinear optical particles.
DOI
The principle of optical trapping is conventionally based on the interaction of optical fields with linear-induced polarizations. However, the optical force originating from the nonlinear polarization becomes significant when nonlinear optical nanoparticles are trapped by femtosecond laser pulses. Herein we develop the time-averaged optical forces on a nonlinear optical nanoparticle using high-repetition-rate femtosecond laser pulses, based on the linear and nonlinear polarization effects. We investigate the dependence of the optical forces on the magnitudes and signs of the refractive nonlinearities. It is found that the self-focusing effect enhances the trapping ability, whereas the self-defocusing effect leads to the splitting of the potential well at the focal plane and destabilizes the optical trap. Our results show good agreement with the reported experimental observations and provide theoretical support for capturing nonlinear optical particles.
DOI
Friday, February 9, 2018
New Characterization of Plasmons in Nanowire Dimers by Optical Forces and Torques
R. M. Abraham Ekeroth
In a previous work, unexpected optical torques were found on metallic dimers of infinite nanowires. The dimers were illuminated with linearly polarized plane waves. Here, the study is extended to bigger systems: the spin torques are induced independently of scale, shape details, and dielectric corrections. New properties appear in the dynamics as the breaking of the action-reaction law, changes in the radiation pressures, or the detection of forbidden modes—dark plasmons—by optical forces. Furthermore, the spectra of spin torques show more resolved resonances than typical far-field spectra. The numerical study is based on an exact method. New possibilities are suggested for the detection of asymmetries in nanostructures. The results are thought for the design of nanorotators and nanodetectors, or simply approach the movement of coupled particles with more accuracy.
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In a previous work, unexpected optical torques were found on metallic dimers of infinite nanowires. The dimers were illuminated with linearly polarized plane waves. Here, the study is extended to bigger systems: the spin torques are induced independently of scale, shape details, and dielectric corrections. New properties appear in the dynamics as the breaking of the action-reaction law, changes in the radiation pressures, or the detection of forbidden modes—dark plasmons—by optical forces. Furthermore, the spectra of spin torques show more resolved resonances than typical far-field spectra. The numerical study is based on an exact method. New possibilities are suggested for the detection of asymmetries in nanostructures. The results are thought for the design of nanorotators and nanodetectors, or simply approach the movement of coupled particles with more accuracy.
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Using light scattering to resolve Brownian rotation dynamics of optically trapped Au nanorods
Ana Andres-Arroyo and Peter J. Reece
Optically trapped Au nanorods are known to adopt a preferential orientation when trapped in three dimensions at the focus of linearly polarised optical tweezers. Trapped nanorods experience both translational and rotational perturbations due to Brownian motion that are governed by the strength of the trap and associated shape-dependent hydrodynamic properties. In this study, we make use of the strong angular dependent light scattering of the localised surface plasmon resonances to interrogate the rotational dynamics of trapped nanorods principally aligned along the propagation axis of the trapping laser. Our measurements reveal that significant rotational dynamics can be observed whilst maintaining stable translational trapping at low powers.
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Optically trapped Au nanorods are known to adopt a preferential orientation when trapped in three dimensions at the focus of linearly polarised optical tweezers. Trapped nanorods experience both translational and rotational perturbations due to Brownian motion that are governed by the strength of the trap and associated shape-dependent hydrodynamic properties. In this study, we make use of the strong angular dependent light scattering of the localised surface plasmon resonances to interrogate the rotational dynamics of trapped nanorods principally aligned along the propagation axis of the trapping laser. Our measurements reveal that significant rotational dynamics can be observed whilst maintaining stable translational trapping at low powers.
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Glia-to-neuron transfer of miRNAs via extracellular vesicles: a new mechanism underlying inflammation-induced synaptic alterations
Ilaria Prada, Martina Gabrielli, Elena Turola, Alessia Iorio, Giulia D’Arrigo, Roberta Parolisi, Mariacristina De Luca, Marco Pacifici, Mattia Bastoni, Marta Lombardi, Giuseppe Legname, Dan Cojoc, Annalisa Buffo, Roberto Furlan, Francesca Peruzzi, Claudia Verderio
Recent evidence indicates synaptic dysfunction as an early mechanism affected in neuroinflammatory diseases, such as multiple sclerosis, which are characterized by chronic microglia activation. However, the mode(s) of action of reactive microglia in causing synaptic defects are not fully understood. In this study, we show that inflammatory microglia produce extracellular vesicles (EVs) which are enriched in a set of miRNAs that regulate the expression of key synaptic proteins. Among them, miR-146a-5p, a microglia-specific miRNA not present in hippocampal neurons, controls the expression of presynaptic synaptotagmin1 (Syt1) and postsynaptic neuroligin1 (Nlg1), an adhesion protein which play a crucial role in dendritic spine formation and synaptic stability. Using a Renilla-based sensor, we provide formal proof that inflammatory EVs transfer their miR-146a-5p cargo to neuron. By western blot and immunofluorescence analysis we show that vesicular miR-146a-5p suppresses Syt1 and Nlg1 expression in receiving neurons. Microglia-to-neuron miR-146a-5p transfer and Syt1 and Nlg1 downregulation do not occur when EV–neuron contact is inhibited by cloaking vesicular phosphatidylserine residues and when neurons are exposed to EVs either depleted of miR-146a-5p, produced by pro-regenerative microglia, or storing inactive miR-146a-5p, produced by cells transfected with an anti-miR-146a-5p. Morphological analysis reveals that prolonged exposure to inflammatory EVs leads to significant decrease in dendritic spine density in hippocampal neurons in vivo and in primary culture, which is rescued in vitro by transfection of a miR-insensitive Nlg1 form. Dendritic spine loss is accompanied by a decrease in the density and strength of excitatory synapses, as indicated by reduced mEPSC frequency and amplitude. These findings link inflammatory microglia and enhanced EV production to loss of excitatory synapses, uncovering a previously unrecognized role for microglia-enriched miRNAs, released in association to EVs, in silencing of key synaptic genes.
DOI
Recent evidence indicates synaptic dysfunction as an early mechanism affected in neuroinflammatory diseases, such as multiple sclerosis, which are characterized by chronic microglia activation. However, the mode(s) of action of reactive microglia in causing synaptic defects are not fully understood. In this study, we show that inflammatory microglia produce extracellular vesicles (EVs) which are enriched in a set of miRNAs that regulate the expression of key synaptic proteins. Among them, miR-146a-5p, a microglia-specific miRNA not present in hippocampal neurons, controls the expression of presynaptic synaptotagmin1 (Syt1) and postsynaptic neuroligin1 (Nlg1), an adhesion protein which play a crucial role in dendritic spine formation and synaptic stability. Using a Renilla-based sensor, we provide formal proof that inflammatory EVs transfer their miR-146a-5p cargo to neuron. By western blot and immunofluorescence analysis we show that vesicular miR-146a-5p suppresses Syt1 and Nlg1 expression in receiving neurons. Microglia-to-neuron miR-146a-5p transfer and Syt1 and Nlg1 downregulation do not occur when EV–neuron contact is inhibited by cloaking vesicular phosphatidylserine residues and when neurons are exposed to EVs either depleted of miR-146a-5p, produced by pro-regenerative microglia, or storing inactive miR-146a-5p, produced by cells transfected with an anti-miR-146a-5p. Morphological analysis reveals that prolonged exposure to inflammatory EVs leads to significant decrease in dendritic spine density in hippocampal neurons in vivo and in primary culture, which is rescued in vitro by transfection of a miR-insensitive Nlg1 form. Dendritic spine loss is accompanied by a decrease in the density and strength of excitatory synapses, as indicated by reduced mEPSC frequency and amplitude. These findings link inflammatory microglia and enhanced EV production to loss of excitatory synapses, uncovering a previously unrecognized role for microglia-enriched miRNAs, released in association to EVs, in silencing of key synaptic genes.
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Ultra-efficient nanoparticle trapping by integrated plasmonic dimers
Aurore Ecarnot, Giovanni Magno, Vy Yam, and Beatrice Dagens
We numerically demonstrate that gold dimers coupled with a silicon-on-insulator waveguide enable an efficient plasmonic tweezing of dielectric nanobeads, having radii down to 50 nm. By means of a rigorous 3D finite difference time domain and simplified gradient force-based calculations, we investigate the effect of the gap size involved on the tweezing action. We also demonstrate that the scattering force helps the trapping in the proximity of the dimer, thanks to the establishment of light vortices.
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We numerically demonstrate that gold dimers coupled with a silicon-on-insulator waveguide enable an efficient plasmonic tweezing of dielectric nanobeads, having radii down to 50 nm. By means of a rigorous 3D finite difference time domain and simplified gradient force-based calculations, we investigate the effect of the gap size involved on the tweezing action. We also demonstrate that the scattering force helps the trapping in the proximity of the dimer, thanks to the establishment of light vortices.
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Nanometer-precision linear sorting with synchronized optofluidic dual barriers
Yuzhi Shi, Sha Xiong, Lip Ket Chin, Jingbo Zhang, Wee Ser, Jiuhui Wu, Tianning Chen, Zhenchuan Yang, Yilong Hao, Bo Liedberg, Peng Huat Yap, Din Ping Tsai, Cheng-Wei Qiu and Ai Qun Liu
The past two decades have witnessed the revolutionary development of optical trapping of nanoparticles, most of which deal with trapping stiffness larger than 10−8 N/m. In this conventional regime, however, it remains a formidable challenge to sort out sub–50-nm nanoparticles with single-nanometer precision, isolating us from a rich flatland with advanced applications of micromanipulation. With an insightfully established roadmap of damping, the synchronization between optical force and flow drag force can be coordinated to attempt the loosely overdamped realm (stiffness, 10−10 to 10−8 N/m), which has been challenging. This paper intuitively demonstrates the remarkable functionality to sort out single gold nanoparticles with radii ranging from 30 to 50 nm, as well as 100- and 150-nm polystyrene nanoparticles, with single nanometer precision. The quasi-Bessel optical profile and the loosely overdamped potential wells in the microchannel enable those aforementioned nanoparticles to be separated, positioned, and microscopically oscillated. This work reveals an unprecedentedly meaningful damping scenario that enriches our fundamental understanding of particle kinetics in intriguing optical systems, and offers new opportunities for tumor targeting, intracellular imaging, and sorting small particles such as viruses and DNA.
DOI
The past two decades have witnessed the revolutionary development of optical trapping of nanoparticles, most of which deal with trapping stiffness larger than 10−8 N/m. In this conventional regime, however, it remains a formidable challenge to sort out sub–50-nm nanoparticles with single-nanometer precision, isolating us from a rich flatland with advanced applications of micromanipulation. With an insightfully established roadmap of damping, the synchronization between optical force and flow drag force can be coordinated to attempt the loosely overdamped realm (stiffness, 10−10 to 10−8 N/m), which has been challenging. This paper intuitively demonstrates the remarkable functionality to sort out single gold nanoparticles with radii ranging from 30 to 50 nm, as well as 100- and 150-nm polystyrene nanoparticles, with single nanometer precision. The quasi-Bessel optical profile and the loosely overdamped potential wells in the microchannel enable those aforementioned nanoparticles to be separated, positioned, and microscopically oscillated. This work reveals an unprecedentedly meaningful damping scenario that enriches our fundamental understanding of particle kinetics in intriguing optical systems, and offers new opportunities for tumor targeting, intracellular imaging, and sorting small particles such as viruses and DNA.
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A switching controller for high speed cell transportation by using a robot-aided optical tweezers system
Xiangpeng Li, Hao Yang, Haibo Huang, Dong Sun
Rapid and efficient cell manipulation is critical to many cellular operations at the single-cell resolution. In this paper, we propose a new approach for high speed manipulation of a single suspended cell using a robot-aided optical tweezers cell manipulation system. A switching geometrical model for achieving automatic cell trapping, maintenance of optical trapping, and obstacle avoidance is developed based on an objective of confining the trapped cell inside the high speed transfer region, which can help attain high speed cell transportation velocity. With the switching geometrical model, a controller for high speed cell transportation is proposed to transfer the target cell to the destination efficiently. Experiments of manipulating human leukemia cancer NB-4 cells to the specific testing area for property characterization are performed to demonstrate the effectiveness of the proposed approach.
DOI
Rapid and efficient cell manipulation is critical to many cellular operations at the single-cell resolution. In this paper, we propose a new approach for high speed manipulation of a single suspended cell using a robot-aided optical tweezers cell manipulation system. A switching geometrical model for achieving automatic cell trapping, maintenance of optical trapping, and obstacle avoidance is developed based on an objective of confining the trapped cell inside the high speed transfer region, which can help attain high speed cell transportation velocity. With the switching geometrical model, a controller for high speed cell transportation is proposed to transfer the target cell to the destination efficiently. Experiments of manipulating human leukemia cancer NB-4 cells to the specific testing area for property characterization are performed to demonstrate the effectiveness of the proposed approach.
DOI
Tuesday, February 6, 2018
Tunable optical forces exerted on a black phosphorus coated dielectric particle by a Gaussian beam
Yang Yang, Xing Jiang, Banxian Ruan, Xiaoyu Dai, and Yuanjiang Xiang
In this paper, we systematically investigate the optical forces exerted on a black phosphorus (BP) coated dielectric particle by a Gaussian beam. The optical forces of the BP coated particle could be modified effectively by tuning the characteristics of the BP layer, such as the carrier density, BP thickness, and the angular dependence of anisotropic conductivity. The resonant mechanism and whispering gallery mode of the BP coated particle are analyzed. Furthermore, the multi-polar surface plasmons of the BP coated dielectric particle excited by the Laguerre Gaussian beam in the infrared band are also investigated. These investigations provide rich potential applications in flexible optical manipulation and optoelectronic devices.
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In this paper, we systematically investigate the optical forces exerted on a black phosphorus (BP) coated dielectric particle by a Gaussian beam. The optical forces of the BP coated particle could be modified effectively by tuning the characteristics of the BP layer, such as the carrier density, BP thickness, and the angular dependence of anisotropic conductivity. The resonant mechanism and whispering gallery mode of the BP coated particle are analyzed. Furthermore, the multi-polar surface plasmons of the BP coated dielectric particle excited by the Laguerre Gaussian beam in the infrared band are also investigated. These investigations provide rich potential applications in flexible optical manipulation and optoelectronic devices.
DOI
Repartitioning of glycerol between levitated and surrounding deposited glycerol/NaNO3/H2O droplets
Xiaoyan Gao, Chen Cai, Jiabi Ma, Yunhong Zhang
Repartitioning of semi-volatile organic compounds (SVOCs) between particles is an important process to understand the particle growth and shrinkage in the atmosphere environment. Here, by using optical tweezers coupled with cavity-enhanced Raman spectroscopy, we report the repartitioning of glycerol between a levitated glycerol/NaNO3/H2O droplet and surrounding glycerol/NaNO3/H2O droplets deposited on the inner wall of a chamber with different organic to inorganic molar ratios (OIRs). For the high OIR with 3 : 1, no NaNO3 crystallization occurs both for levitated and deposited droplets in the whole relative humidity (RH) range, the radius of the levitated droplet decreases slowly due to the evaporation of glycerol from the levitated droplet at constant RHs. The levitated droplets radii with OIR of 1 : 1 and 1 : 3 increase with constant RHs that are lower than 45.3% and 55.7%, respectively, indicating that the repartitioning of glycerol occurs. The reason is that NaNO3 in the deposited droplets is crystallized when RH is lower than 45.3% for 1 : 1 or 55.7% for 1 : 3. So the vapour pressure of glycerol at the surface of deposited droplets is higher than that of the levitated droplet which always remains as liquid droplet without NaNO3 crystallization, resulting in the transfer of glycerol from the deposited ones to the levitated one. The process of the glycerol repartitioning we discussed herein is a useful model to interpret the repartitioning of SVOCs between the externally mixed particles with different phase states.
DOI
Repartitioning of semi-volatile organic compounds (SVOCs) between particles is an important process to understand the particle growth and shrinkage in the atmosphere environment. Here, by using optical tweezers coupled with cavity-enhanced Raman spectroscopy, we report the repartitioning of glycerol between a levitated glycerol/NaNO3/H2O droplet and surrounding glycerol/NaNO3/H2O droplets deposited on the inner wall of a chamber with different organic to inorganic molar ratios (OIRs). For the high OIR with 3 : 1, no NaNO3 crystallization occurs both for levitated and deposited droplets in the whole relative humidity (RH) range, the radius of the levitated droplet decreases slowly due to the evaporation of glycerol from the levitated droplet at constant RHs. The levitated droplets radii with OIR of 1 : 1 and 1 : 3 increase with constant RHs that are lower than 45.3% and 55.7%, respectively, indicating that the repartitioning of glycerol occurs. The reason is that NaNO3 in the deposited droplets is crystallized when RH is lower than 45.3% for 1 : 1 or 55.7% for 1 : 3. So the vapour pressure of glycerol at the surface of deposited droplets is higher than that of the levitated droplet which always remains as liquid droplet without NaNO3 crystallization, resulting in the transfer of glycerol from the deposited ones to the levitated one. The process of the glycerol repartitioning we discussed herein is a useful model to interpret the repartitioning of SVOCs between the externally mixed particles with different phase states.
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Fabrication and characterization of machined multi-core fiber tweezers for single cell manipulation
Georgia Anastasiadi, Mark Leonard, Lynn Paterson, and William N. Macpherson
Optical tweezing is a non-invasive technique that can enable a variety of single cell experiments; however, it tends to be based on a high numerical aperture (NA) microscope objective to both deliver the tweezing laser light and image the sample. This introduces restrictions in system flexibility when both trapping and imaging. Here, we demonstrate a novel, high NA tweezing system based on micro-machined multicore optical fibers. Using the machined, multicore fiber tweezer, cells are optically manipulated under a variety of microscopes, without requiring a high NA objective lens. The maximum NA of the fiber-based tweezer demonstrated is 1.039. A stable trap with a maximum total power 30 mW has been characterized to exert a maximum optical force of 26.4 pN, on a trapped, 7 μm diameter yeast cell. Single cells are held 15-35 μm from the fiber end and can be manipulated in the x, y and z directions throughout the sample. In this way, single cells are controllably trapped under a Raman microscope to categorize the yeast cells as live or dead, demonstrating trapping by the machined multicore fiber-based tweezer decoupled from the imaging or excitation objective lens.
DOI
Optical tweezing is a non-invasive technique that can enable a variety of single cell experiments; however, it tends to be based on a high numerical aperture (NA) microscope objective to both deliver the tweezing laser light and image the sample. This introduces restrictions in system flexibility when both trapping and imaging. Here, we demonstrate a novel, high NA tweezing system based on micro-machined multicore optical fibers. Using the machined, multicore fiber tweezer, cells are optically manipulated under a variety of microscopes, without requiring a high NA objective lens. The maximum NA of the fiber-based tweezer demonstrated is 1.039. A stable trap with a maximum total power 30 mW has been characterized to exert a maximum optical force of 26.4 pN, on a trapped, 7 μm diameter yeast cell. Single cells are held 15-35 μm from the fiber end and can be manipulated in the x, y and z directions throughout the sample. In this way, single cells are controllably trapped under a Raman microscope to categorize the yeast cells as live or dead, demonstrating trapping by the machined multicore fiber-based tweezer decoupled from the imaging or excitation objective lens.
DOI
Pulling Membrane Nanotubes from Giant Unilamellar Vesicles
Coline Prévost, Feng-Ching Tsai, Patricia Bassereau, Mijo Simunovic
Many proteins in the cell sense and induce membrane curvature. We describe a method to pull membrane nanotubes from lipid vesicles to study the interaction of proteins or any curvature-active molecule with curved membranes in vitro.
DOI
Many proteins in the cell sense and induce membrane curvature. We describe a method to pull membrane nanotubes from lipid vesicles to study the interaction of proteins or any curvature-active molecule with curved membranes in vitro.
DOI
Hyperstretching DNA
Koen Schakenraad, Andreas S. Biebricher, Maarten Sebregts, Brian ten Bensel, Erwin J. G. Peterman, Gijs J. L. Wuite, Iddo Heller, Cornelis Storm & Paul van der Schoot
The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely used in biophysical/chemical assays and drug treatments. We present single-molecule experiments and a three-state statistical mechanical model that provide a quantitative understanding of the interplay between B-DNA, overstretched DNA and intercalated DNA. The predictions of this model include a hitherto unconfirmed hyperstretched state, twice the length of B-DNA. Our force-fluorescence experiments confirm this hyperstretched state and reveal its sequence dependence. These results pin down the physical principles that govern DNA mechanics under the influence of tension and biochemical reactions. A predictive understanding of the possibilities and limitations of DNA extension can guide refined exploitation of DNA in, e.g., programmable soft materials and DNA origami applications.
DOI
The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely used in biophysical/chemical assays and drug treatments. We present single-molecule experiments and a three-state statistical mechanical model that provide a quantitative understanding of the interplay between B-DNA, overstretched DNA and intercalated DNA. The predictions of this model include a hitherto unconfirmed hyperstretched state, twice the length of B-DNA. Our force-fluorescence experiments confirm this hyperstretched state and reveal its sequence dependence. These results pin down the physical principles that govern DNA mechanics under the influence of tension and biochemical reactions. A predictive understanding of the possibilities and limitations of DNA extension can guide refined exploitation of DNA in, e.g., programmable soft materials and DNA origami applications.
DOI
Single-molecule techniques in biophysics: a review of the progress in methods and applications
Helen Miller, Zhaokun Zhou, Jack Shepherd, Adam J M Wollman and Mark C Leake
Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in 'force spectroscopy' techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.
DOI
Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in 'force spectroscopy' techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.
DOI
Friday, February 2, 2018
Rapid localized crystallization of lysozyme by laser trapping
Ken-ichi Yuyama, Kai-Di Chang, Jing-Ru Tu, Hiroshi Masuhara and Teruki Sugiyama
Confining protein crystallization to a millimetre size was achieved within 0.5 h after stopping 1 h intense trapping laser irradiation, which shows excellent performance in spatial and temporal controllability compared to spontaneous nucleation. A continuous-wave near-infrared laser beam is tightly focused into a glass/solution interfacial layer of a supersaturated buffer solution of hen egg-white lysozyme (HEWL). The crystallization is not observed during laser trapping, but initiated by stopping the laser irradiation. The generated crystals are localized densely in a circular area with a diameter of a few millimetres around the focal spot and show specific directions of the optical axes of the HEWL crystals. To interpret this unique crystallization, we propose a mechanism that nucleation and the subsequent growth take place in a highly concentrated domain consisting of HEWL liquid-like clusters after turning off laser trapping.
DOI
Confining protein crystallization to a millimetre size was achieved within 0.5 h after stopping 1 h intense trapping laser irradiation, which shows excellent performance in spatial and temporal controllability compared to spontaneous nucleation. A continuous-wave near-infrared laser beam is tightly focused into a glass/solution interfacial layer of a supersaturated buffer solution of hen egg-white lysozyme (HEWL). The crystallization is not observed during laser trapping, but initiated by stopping the laser irradiation. The generated crystals are localized densely in a circular area with a diameter of a few millimetres around the focal spot and show specific directions of the optical axes of the HEWL crystals. To interpret this unique crystallization, we propose a mechanism that nucleation and the subsequent growth take place in a highly concentrated domain consisting of HEWL liquid-like clusters after turning off laser trapping.
DOI
Force and Scale Dependence of the Elasticity of Self-Assembled DNA Bottle Brushes
Márcio Santos Rocha, Ingeborg M. Storm, Raniella Falchetto Bazoni, Ésio Bessa Ramos, Armando Hernandez-Garcia, Martien A. Cohen Stuart, Frans Leermakers , and Renko de Vries
As a model system to study the elasticity of bottle-brush polymers, we here introduce self-assembled DNA bottle brushes, consisting of a DNA main chain that can be very long and still of precisely defined length, and precisely monodisperse polypeptide side chains that are physically bound to the DNA main chains. Polypeptide side chains have a diblock architecture, where one block is a small archaeal nucleoid protein Sso7d that strongly binds to DNA. The other block is a net neutral, hydrophilic random coil polypeptide with a length of exactly 798 amino acids. Light scattering shows that for saturated brushes the grafting density is one side chain per 5.6 nm of DNA main chain. According to small-angle X-ray scattering, the brush diameter is D = 17 nm. By analyzing configurations of adsorbed DNA bottle brushes using AFM, we find that the effective persistence of the saturated DNA bottle brushes is Peff = 95 nm, but from force–extension curves of single DNA bottle brushes measured using optical tweezers we find Peff = 15 nm. The latter is equal to the value expected for DNA coated by the Sso7d binding block alone. The apparent discrepancy between the two measurements is rationalized in terms of the scale dependence of the bottle-brush elasticity using theory previously developed to analyze the scale-dependent electrostatic stiffening of DNA at low ionic strengths.
DOI
As a model system to study the elasticity of bottle-brush polymers, we here introduce self-assembled DNA bottle brushes, consisting of a DNA main chain that can be very long and still of precisely defined length, and precisely monodisperse polypeptide side chains that are physically bound to the DNA main chains. Polypeptide side chains have a diblock architecture, where one block is a small archaeal nucleoid protein Sso7d that strongly binds to DNA. The other block is a net neutral, hydrophilic random coil polypeptide with a length of exactly 798 amino acids. Light scattering shows that for saturated brushes the grafting density is one side chain per 5.6 nm of DNA main chain. According to small-angle X-ray scattering, the brush diameter is D = 17 nm. By analyzing configurations of adsorbed DNA bottle brushes using AFM, we find that the effective persistence of the saturated DNA bottle brushes is Peff = 95 nm, but from force–extension curves of single DNA bottle brushes measured using optical tweezers we find Peff = 15 nm. The latter is equal to the value expected for DNA coated by the Sso7d binding block alone. The apparent discrepancy between the two measurements is rationalized in terms of the scale dependence of the bottle-brush elasticity using theory previously developed to analyze the scale-dependent electrostatic stiffening of DNA at low ionic strengths.
DOI
Derivation of nearest-neighbor DNA parameters in magnesium from single molecule experiments
Josep Maria Huguet, Marco Ribezzi-Crivellari, Cristiano Valim Bizarro, Felix Ritort
DNA hybridization is an essential molecular reaction in biology with many applications. The nearest-neighbor (NN) model for nucleic acids predicts DNA thermodynamics using energy values for the different base pair motifs. These values have been derived from melting experiments in monovalent and divalent salt and applied to predict melting temperatures of oligos within a few degrees. However, an improved determination of the NN energy values and their salt dependencies in magnesium is still needed for current biotechnological applications seeking high selectivity in the hybridization of synthetic DNAs. We developed a methodology based on single molecule unzipping experiments to derive accurate NN energy values and initiation factors for DNA. A new set of values in magnesium is derived, which reproduces unzipping data and improves melting temperature predictions for all available oligo lengths, in a range of temperature and salt conditions where correlation effects between the magnesium bound ions are weak. The NN salt correction parameters are shown to correlate to the GC content of the NN motifs. Our study shows the power of single-molecule force spectroscopy assays to unravel novel features of nucleic acids such as sequence-dependent salt corrections.
DOI
DNA hybridization is an essential molecular reaction in biology with many applications. The nearest-neighbor (NN) model for nucleic acids predicts DNA thermodynamics using energy values for the different base pair motifs. These values have been derived from melting experiments in monovalent and divalent salt and applied to predict melting temperatures of oligos within a few degrees. However, an improved determination of the NN energy values and their salt dependencies in magnesium is still needed for current biotechnological applications seeking high selectivity in the hybridization of synthetic DNAs. We developed a methodology based on single molecule unzipping experiments to derive accurate NN energy values and initiation factors for DNA. A new set of values in magnesium is derived, which reproduces unzipping data and improves melting temperature predictions for all available oligo lengths, in a range of temperature and salt conditions where correlation effects between the magnesium bound ions are weak. The NN salt correction parameters are shown to correlate to the GC content of the NN motifs. Our study shows the power of single-molecule force spectroscopy assays to unravel novel features of nucleic acids such as sequence-dependent salt corrections.
DOI
Controllable Swarming and Assembly of Micro/Nanomachines
Conghui Liu, Tailin Xu, Li-Ping Xu and Xueji Zhang
Motion is a common phenomenon in biological processes. Major advances have been made in designing various self-propelled micromachines that harvest different types of energies into mechanical movement to achieve biomedicine and biological applications. Inspired by fascinating self-organization motion of natural creatures, the swarming or assembly of synthetic micro/nanomachines (often referred to micro/nanoswimmers, micro/nanorobots, micro/nanomachines, or micro/nanomotors), are able to mimic these amazing natural systems to help humanity accomplishing complex biological tasks. This review described the fuel induced methods (enzyme, hydrogen peroxide, hydrazine, et al.) and fuel-free induced approaches (electric, ultrasound, light, and magnetic) that led to control the assembly and swarming of synthetic micro/nanomachines. Such behavior is of fundamental importance in improving our understanding of self-assembly processes that are occurring on molecular to macroscopic length scales.
DOI
Motion is a common phenomenon in biological processes. Major advances have been made in designing various self-propelled micromachines that harvest different types of energies into mechanical movement to achieve biomedicine and biological applications. Inspired by fascinating self-organization motion of natural creatures, the swarming or assembly of synthetic micro/nanomachines (often referred to micro/nanoswimmers, micro/nanorobots, micro/nanomachines, or micro/nanomotors), are able to mimic these amazing natural systems to help humanity accomplishing complex biological tasks. This review described the fuel induced methods (enzyme, hydrogen peroxide, hydrazine, et al.) and fuel-free induced approaches (electric, ultrasound, light, and magnetic) that led to control the assembly and swarming of synthetic micro/nanomachines. Such behavior is of fundamental importance in improving our understanding of self-assembly processes that are occurring on molecular to macroscopic length scales.
DOI
Single-Molecule Mechanochemical pH Sensing Revealing the Proximity Effect of Hydroniums Generated by an Alkaline Phosphatase
Prakash Shrestha, Yunxi Cui, Jia Wei, Sagun Jonchhe, and Hanbin Mao
Due to the fast diffusion, small molecules such as hydronium ions (H3O+) are expected to be homogeneously distributed, even close to the site-of-origin. Given the importance of H3O+ in numerous processes, it is surprising that H3O+ concentration ([H3O+]) has yet to be profiled near its generation site with nanometer resolution. Here, we innovated a single-molecule method to probe [H3O+] in nanometer proximity of individual alkaline phosphatases. We designed a mechanophore with cytosine (C)–C mismatch pairs in a DNA hairpin. Binding of H3O+ to these C–C pairs changes mechanical properties, such as stability and transition distance, of the mechanophore. These changes are recorded in optical tweezers and analyzed in a multivariate fashion to reduce the stochastic noise of individual mechanophores. With this method, we found [H3O+] increases in the nanometer vicinity of an active alkaline phosphatase, which supports that the proximity effect is the cause for increased rates in cascade enzymatic reactions.
DOI
Due to the fast diffusion, small molecules such as hydronium ions (H3O+) are expected to be homogeneously distributed, even close to the site-of-origin. Given the importance of H3O+ in numerous processes, it is surprising that H3O+ concentration ([H3O+]) has yet to be profiled near its generation site with nanometer resolution. Here, we innovated a single-molecule method to probe [H3O+] in nanometer proximity of individual alkaline phosphatases. We designed a mechanophore with cytosine (C)–C mismatch pairs in a DNA hairpin. Binding of H3O+ to these C–C pairs changes mechanical properties, such as stability and transition distance, of the mechanophore. These changes are recorded in optical tweezers and analyzed in a multivariate fashion to reduce the stochastic noise of individual mechanophores. With this method, we found [H3O+] increases in the nanometer vicinity of an active alkaline phosphatase, which supports that the proximity effect is the cause for increased rates in cascade enzymatic reactions.
DOI
Geometrical effect characterization of femtosecond-laser manufactured glass microfluidic chips based on optical manipulation of submicroparticles
Domna G. Kotsifaki; Mark D. Mackenzie; Georgia Polydefki; Ajoy K. Kar; Mersini Makropoulou; Alexandros A. Serafetinides
Microfluidic devices provide a platform with wide ranging applications from environmental monitoring to disease diagnosis. They offer substantive advantages but are often not optimized or designed to be used by nonexpert researchers. Microchannels of a microanalysis platform and their geometrical characterization are of eminent importance when designing such devices. We present a method that is used to optimize each microchannel within a device using high-throughput particle manipulation. For this purpose, glass-based microfluidic devices, with three-dimensional channel networks of several geometrical sizes, were fabricated by employing laser fabrication techniques. The effect of channel geometry was investigated by employing an optical tweezer. The optical trapping force depends on the flow velocity that is associated with the dimensions of the microchannel. We observe a linear dependence of the trapping efficiency and of the fluid flow velocity, with the channel dimensions. We determined that the highest trapping efficiency was achieved for microchannels with aspect ratio equal to one. Numerical simulation validated the impact of the device design dimensions on the trapping efficiency. This investigation indicates that the geometrical characteristics, the flow velocity, and trapping efficiency are crucial and should be considered when fabricating microfluidic devices for cell studies.
DOI
Microfluidic devices provide a platform with wide ranging applications from environmental monitoring to disease diagnosis. They offer substantive advantages but are often not optimized or designed to be used by nonexpert researchers. Microchannels of a microanalysis platform and their geometrical characterization are of eminent importance when designing such devices. We present a method that is used to optimize each microchannel within a device using high-throughput particle manipulation. For this purpose, glass-based microfluidic devices, with three-dimensional channel networks of several geometrical sizes, were fabricated by employing laser fabrication techniques. The effect of channel geometry was investigated by employing an optical tweezer. The optical trapping force depends on the flow velocity that is associated with the dimensions of the microchannel. We observe a linear dependence of the trapping efficiency and of the fluid flow velocity, with the channel dimensions. We determined that the highest trapping efficiency was achieved for microchannels with aspect ratio equal to one. Numerical simulation validated the impact of the device design dimensions on the trapping efficiency. This investigation indicates that the geometrical characteristics, the flow velocity, and trapping efficiency are crucial and should be considered when fabricating microfluidic devices for cell studies.
DOI
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