Friday, September 30, 2016

Particle-Based Modeling of Living Actin Filaments in an Optical Trap

Thomas A. Hunt, Santosh Mogurampelly, Giovanni Ciccotti, Carlo Pierleoni, and Jean-Paul Ryckaert

We report a coarse-grained molecular dynamics simulation study of a bundle of parallel actin filaments under supercritical conditions pressing against a loaded mobile wall using a particle-based approach where each particle represents an actin unit. The filaments are grafted to a fixed wall at one end and are reactive at the other end, where they can perform single monomer (de)polymerization steps and push on a mobile obstacle. We simulate a reactive grand canonical ensemble in a box of fixed transverse area A, with a fixed number of grafted filaments Nf , at temperature T and monomer chemical potential μ1 . For a single filament case ( Nf=1 ) and for a bundle of Nf=8 filaments, we analyze the structural and dynamical properties at equilibrium where the external load compensates the average force exerted by the bundle. The dynamics of the bundle-moving-wall unit are characteristic of an over-damped Brownian oscillator in agreement with recent in vitro experiments by an optical trap setup. We analyze the influence of the pressing wall on the kinetic rates of (de)polymerization events for the filaments. Both static and dynamic results compare reasonably well with recent theoretical treatments of the same system. Thus, we consider the proposed model as a good tool to investigate the properties of a bundle of living filaments.


CO2 Biofixation of Actinobacillus succinogenes Through Novel Amine-Functionalized Polystyrene Microsphere Materials

Wenhao Zhu, Qiang Li, Ning Dai

CO2-derived succinate production was enhanced by Actinobacillus succinogenes through polystyrene (PSt) microsphere materials for CO2 adsorption in bioreactor, and the adhesion forces between A. succinogenes bacteria and PSt materials were characterized. Synthesized uniformly sized and highly cross-linked PSt microspheres had high specific surface areas. After modification with amine functional groups, the novel amine-functionalized PSt microspheres exhibited a high adsorption capacity of 25.3 mg CO2/g materials. After addition with the functionalized microspheres into the culture broth, CO2 supply to the cells increased. Succinate production by A. succinogenes can be enhanced from 29.6 to 48.1 g L−1. Moreover, the characterization of interaction forces between A. succinogenes cells and the microspheres indicated that the maximal adhesive force was about 250 pN. The amine-functionalized PSt microspheres can adsorb a large amount of CO2 and be employed for A. succinogenes anaerobic cultivation in bioreactor for high-efficiency production of CO2-derived succinate.


Improving Sensitivity and Reproducibility of SERS Sensing in Microenvironments Using Individual, Optically Trapped SERS Probes

Pietro Strobbia, Adam Mayer, Brian M Cullum

Surface-enhanced Raman spectroscopy (SERS) sensors offer many advantages for chemical analyses, including the ability to provide chemical specific information and multiplexed detection capability at specific locations. However, to have operative SERS sensors for probing microenvironments, probes with high signal enhancement and reproducibility are necessary. To this end, dynamic enhancement of SERS (i.e., in-situ amplification of signal-to-noise and signal-to-background ratios) from individual probes has been explored. In this paper, we characterize the use of optical tweezers to amplify SERS signals as well as suppress background signals via trapping of individual SERS active probes. This amplification is achieved through a steady presence of a single “hot” particle in the focus of the excitation laser. In addition to increases in signal and concomitant decreases in non-SERS backgrounds, optical trapping results in an eightfold increase in the stability of the signal as well. This enhancement strategy was demonstrated using both single and multilayered SERS sub-micron probes, producing combined signal enhancements of 24-fold (beyond the native 106 SERS enhancement) for a three-layered geometry. The ability to dynamically control the enhancement offers the possibility to develop SERS-based sensors and probes with tailored sensitivities. In addition, since this trapping enhancement can be used to observe individual probes with low laser fluences, it could offer particular interest in probing the composition of microenvironments not amenable to tip-enhanced Raman spectroscopy or other scanning probe methods (e.g., intracellular analyses, etc.).


Mechanochemical Sensing of Single and Few Hg(II) Ions Using Polyvalent Principles

Shankar Mandal, Sangeetha Selvam, Prakash Shrestha, and Hanbin Mao

Sensitivity of biosensors is set by the dissociation constant (Kd) between analytes and probes. Although potent amplification steps can be accommodated between analyte recognition and signal transduction in a sensor to improve the sensitivity 4–6 orders of magnitude below Kd, they compromise temporal resolution. Here, we demonstrated mechanochemical sensing that broke the Kd limit by 9 orders of magnitude for Hg detection without amplifications. Analogous to trawl fishing, we introduced multiple Hg binding units (thymine (T)–T pairs) in a molecular trawl made of two poly-T strands. Inspired by dipsticks to gauge content levels, mechanical information (force/extension) of a DNA hairpin dipstick was used to measure the single or few Hg2+ ions bound to the molecular trawl, which was levitated by two optically trapped particles. The multivalent binding and single-molecule sensitivity allowed us to detect unprecedented 1 fM Hg ions in 20 min in field samples treated by simple filtrations.


Thursday, September 29, 2016

Tension-Dependent Free Energies of Nucleosome Unwrapping

Joshua Lequieu, Andrés Córdoba, David C. Schwartz, and Juan J. de Pablo
Nucleosomes form the basic unit of compaction within eukaryotic genomes, and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a central problem in biophysics and is critical to understanding how nucleosome positions influence gene expression. By comparing to single-molecule experiments, we demonstrate that a coarse-grained molecular model of the nucleosome can reproduce key aspects of nucleosome unwrapping. Using detailed simulations of DNA and histone proteins, we calculate the tension-dependent free energy surface corresponding to the unwrapping process. The model reproduces quantitatively the forces required to unwrap the nucleosome and reveals the role played by electrostatic interactions during this process. We then demonstrate that histone modifications and DNA sequence can have significant effects on the energies of nucleosome formation. Most notably, we show that histone tails contribute asymmetrically to the stability of the outer and inner turn of nucleosomal DNA and that depending on which histone tails are modified, the tension-dependent response is modulated differently.


Optically assembled droplet interface bilayer (OptiDIB) networks from cell-sized microdroplets

Mark S. Friddin, Guido Bolognesi, Yuval Elani, Nicholas J. Brooks, Robert V. Law, John M. Seddon, Mark A. A. Neil and Oscar Ces

We report a new platform technology to systematically assemble droplet interface bilayer (DIB) networks in user-defined 3D architectures from cell-sized droplets using optical tweezers. Our OptiDIB platform is the first demonstration of optical trapping to precisely construct 3D DIB networks, paving the way for the development of a new generation of modular bio-systems.


Temporal oscillations of light transmission through dielectric microparticles subjected to optically induced motion

Almas F. Sadreev and E. Ya. Sherman

We consider light-induced binding and motion of dielectric microparticles in an optical waveguide that gives rise to a backaction effect such as light transmission oscillating with time. Modeling the particles by dielectric slabs allows us to solve the problem analytically and obtain a rich variety of dynamical regimes both for Newtonian and damped motion. This variety is clearly reflected in temporal oscillations of the light transmission. The characteristic frequencies of the oscillations are within the ultrasound range of the order of 105 kHz for micron-size particles and injected power of the order of 100 mW. In addition, we consider dynamics of a dielectric particle, driven by light propagating inside a Fabry-Perot resonator. These phenomena pave a way for optical driving and monitoring of the motion of particles in waveguides and resonators.


Direct measurement of optical-trap-induced decoherence

Nobuyuki Matsumoto, Kentaro Komori, Sosuke Ito, Yuta Michimura, and Yoichi Aso

Thermal decoherence is a major obstacle to the realization of quantum coherence for massive mechanical oscillators. Although optical trapping has been used to reduce the thermal decoherence rate for such oscillators, it also increases the rate by subjecting the oscillator to stochastic forces resulting from the frequency fluctuations of the optical field, thereby setting a fundamental limit on the reduction. This is analogous to the noise penalty in an active feedback system. Here, we directly measure the rethermalization process for an initially cooled and optically trapped suspended mirror, and identify the current limiting decoherence rate as due to the optical trap. Our experimental study of the trap-induced decoherence rate will enable future advances in the probing of fundamental quantum mechanics in the bad-cavity regime, such as testing of deformed commutators.


Wednesday, September 28, 2016

Elastic Properties of Nucleic Acids by Single-Molecule Force Spectroscopy

Joan Camunas-Soler, Marco Ribezzi-Crivellari, and Felix Ritort

We review the current knowledge on the use of single-molecule force spectroscopy techniques to extrapolate the elastic properties of nucleic acids. We emphasize the lesser-known elastic properties of single-stranded DNA. We discuss the importance of accurately determining the elastic response in pulling experiments, and we review the simplest models used to rationalize the experimental data as well as the experimental approaches used to pull single-stranded DNA. Applications used to investigate DNA conformational transitions and secondary structure formation are also highlighted. Finally, we provide an overview of the effects of salt and temperature and briefly discuss the effects of contour length and sequence dependence.


Erythrocytes and their role as health indicator: Using structure in a patient-orientated precision medicine approach

Etheresia Pretorius, Oore-ofe O. Olumuyiwa-Akeredolu, Sthembile Mbotwe, Janette Bester

The relevance of erythrocyte light microscopy analysis (a well-known haematological method) is under the spotlight, however there is a place for innovative electron microscopy, (together with biochemical markers) in a pathology laboratory. Inflammation is a key indicator of the health status and erythrocytes are extremely sensitive to oxidative stress or cytokine upregulation, which typically accompany systemic inflammation in most diseases. They are probably the most adaptable cells, and due to their short lifespan, may form a vital indicator of health, and could play a central part in tracking disease and treatment. As the NIH is proposing a precision medicine approach and because individualised medicine should form an essential part in diagnosis and treatment, biophysical combined with biochemical analysis of erythrocytes may be a novel method to track the inflammatory status before and after treatment. This will allow a fully individualised patient orientated precision medicine approach, where one-medication-regime-fits-all is no longer appropriate.


Autoenhanced Raman Spectroscopy via Plasmonic Trapping for Molecular Sensing

Soonwoo Hong, On Shim, Hyosung Kwon, and Yeonho Choi

As a label-free and sensitive biosensor, surface-enhanced Raman spectroscopy (SERS) is a rapidly emerging technique. However, because SERS spectra are obtained in the area of light excitation and the enhancement effect can be varied depending on the position of a substrate, it is important to match the enhanced area with an illuminated spot. Here, in order to overcome such difficulty, we demonstrated a new technique combining SERS with plasmonic trapping. By plasmonic trapping, we can collect gold nanoparticles (GNPs) in the middle of initially fabricated nanobowtie structures where a laser is excited. As a result of trapping GNPs, hot-spots are formed at that area. Because SERS is measured in the area irradiated by a laser, hot-spot can be simultaneously coincided with a detection site for SERS. By using this, we detected Rhodamine 6G to 100 pM. To further verify and improve the reproducibility of our technique, we also calculated the electric field distribution, trapping force and trapping potential.


Negative optical spin torque wrench of a non-diffracting non-paraxial fractional Bessel vortex beam

F.G. Mitri

An absorptive Rayleigh dielectric sphere in a non-diffracting non-paraxial fractional Bessel vortex beam experiences a spin torque. The axial and transverse radiation spin torque components are evaluated in the dipole approximation using the radiative correction of the electric field. Particular emphasis is given on the polarization as well as changing the topological charge α and the half-cone angle of the beam. When α is zero, the axial spin torque component vanishes. However, when α becomes a real positive number, the vortex beam induces left-handed (negative) axial spin torque as the sphere shifts off-axially from the center of the beam. The results show that a non-diffracting non-paraxial fractional Bessel vortex beam is capable of inducing a spin reversal of an absorptive Rayleigh sphere placed arbitrarily in its path. Potential applications are yet to be explored in particle manipulation, rotation in optical tweezers, optical tractor beams, and the design of optically-engineered metamaterials to name a few areas.


Tuesday, September 27, 2016

Identification of volume phase transition of a single microgel particle using optical tweezers

D Karthickeyan, Deepak K Gupta and B V R Tata

Poly (N-isopropyl acrylamide-co-acrylic acid) (PNIPAM-co-Aac) microgel particles are pH responsive and exhibit volume phase transition (VPT) upon variation of pH. Dynamic light scattering (DLS) is used conventionally to identify VPT and requires a dilute suspension with particle concentration ~107 particles cm−3 and if particles are polydisperse in nature, DLS data interpretation is relatively difficult. Here we show that optical tweezers allow one to measure the VPT of a single microgel particle by measuring the optical trap stiffness, κ of trapped particle as a function of pH. We report here a sudden change in κ at VPT, which is shown to arise from a sudden decrease in particle diameter with a concomitant increase in the refractive index of the particle at VPT.


Stable, Free-space Optical Trapping and Manipulation of Sub-micron Particles in an Integrated Microfluidic Chip

Jisu Kim & Jung H. Shin

We demonstrate stable, free-space optical trapping and manipulation in an integrated microfluidic chip using counter-propagating beams. An inverted ridge-type waveguide made of SU8 is cut across by an open trench. The design of the waveguide provides low propagation losses and small divergence of the trapping beam upon emergence from the facet, and the trench designed to be deeper and wider than the optical mode enables full utilization of the optical power with an automatic alignment for counter-propagating beams in a trap volume away from all surfaces. After integration with polydimethylsiloxane (PDMS) microfluidic channel for particle delivery, 0.65 μm and 1 μm diameter polystyrene beads were trapped in free space in the trench, and manipulated to an arbitrary position between the waveguides with a resolution of < 100 nm. Comparison with numerical simulations confirm stable trapping of sub-micron particles, with a 10 kBT threshold power of less than 1 mW and a stiffness that can be 1 order of magnitude larger than that of comparable fiber-based trapping methods.


Single-molecule dissection of stacking forces in DNA

Fabian Kilchherr, Christian Wachauf, Benjamin Pelz, Matthias Rief, Martin Zacharias, Hendrik Dietz

We directly measured at the single-molecule level the forces and lifetimes of DNA base-pair stacking interactions for all stack sequence combinations. Our experimental approach combined dual-beam optical tweezers with DNA origami components to allow positioning of blunt-end DNA helices so that the weak stacking force could be isolated. Base-pair stack arrays that lacked a covalent backbone connection spontaneously dissociated at average rates ranging from 0.02 to 500 per second, depending on the sequence combination and stack array size. Forces in the range from 2 to 8 piconewtons that act along the helical direction only mildly accelerated the stochastic unstacking process. The free-energy increments per stack that we estimate from the measured forward and backward kinetic rates ranged from –0.8 to –3.4 kilocalories per mole, depending on the sequence combination. Our data contributes to understanding the mechanics of DNA processing in biology, and it is helpful for designing the kinetics of DNA-based nanoscale devices according to user specifications.


Coupling rotational and translational motion via a continuous measurement in an optomechanical sphere

Jason F. Ralph, Kurt Jacobs, and Jonathon Coleman

We consider a measurement of the position of a spot painted on the surface of a trapped nano-optomechanical sphere. The measurement extracts information about the position of the spot and in doing so measures a combination of the orientation and position of the sphere. The quantum backaction of the measurement entangles and correlates these two degrees of freedom. Such a measurement is not available for atoms or ions and provides a mechanism to probe the quantum mechanical properties of trapped optomechanical spheres. In performing simulations of this measurement process we also test a numerical method introduced recently by Rouchon and collaborators [H. Amini, M. Mirrahimi, and P. Rouchon, in Proceedings of the 50th IEEE Conference on Decision and Control (CDC, 2011), pp. 6242–6247; P. Rouchon and J. F. Ralph, Phys. Rev. A 91, 012118 (2015)] for solving stochastic master equations. This method guarantees the positivity of the density matrix when the Lindblad operators for all simultaneous continuous measurements are mutually commuting. We show that it is both simpler and far more efficient than previous methods.


Fabrication of quartz microcylinders by laser interference lithography for angular optical tweezers

Zhanna Santybayeva ; Afaf Meghit ; Rudy Desgarceaux ; Roland Teissier ; Frederic Pichot ; Charles de Marin ; Benoit Charlot ; Francesco Pedaci

The use of optical tweezers (OTs) and spin angular momentum transfer to birefringent particles allows new mechanical measurements in systems where torque and rotation are relevant parameters at the single-molecule level. There is a growing interest in developing simple, fast, and inexpensive protocols to produce a large number of submicron scale cylinders of quartz, a positive uniaxial birefringent crystal, to be employed for such angular measurements in OTs. Here, we show that laser interference lithography, a method well known for its simplicity, fulfills these requirements and produces quartz cylindrical particles that we successfully use to apply and measure optical torque in the piconewton nm range in an optical torque wrench.


Friday, September 23, 2016

Fibrin Networks Support Recurring Mechanical Loads by Adapting their Structure across Multiple Scales

Nicholas A. Kurniawan, Bart E. Vos, Andreas Biebricher, Gijs J.L. Wuite, Erwin J.G. Peterman, Gijsje H. Koenderink

Tissues and cells sustain recurring mechanical loads that span a wide range of loading amplitudes and timescales as a consequence of exposure to blood flow, muscle activity, and external impact. Both tissues and cells derive their mechanical strength from fibrous protein scaffolds, which typically have a complex hierarchical structure. In this study, we focus on a prototypical hierarchical biomaterial, fibrin, which is one of the most resilient naturally occurring biopolymers and forms the structural scaffold of blood clots. We show how fibrous networks composed of fibrin utilize irreversible changes in their hierarchical structure at different scales to maintain reversible stress stiffening up to large strains. To trace the origin of this paradoxical resilience, we systematically tuned the microstructural parameters of fibrin and used a combination of optical tweezers and fluorescence microscopy to measure the interactions of single fibrin fibers for the first time, to our knowledge. We demonstrate that fibrin networks adapt to moderate strains by remodeling at the network scale through the spontaneous formation of new bonds between fibers, whereas they adapt to high strains by plastic remodeling of the fibers themselves. This multiscale adaptation mechanism endows fibrin gels with the remarkable ability to sustain recurring loads due to shear flows and wound stretching. Our findings therefore reveal a microscopic mechanism by which tissues and cells can balance elastic nonlinearity and plasticity, and thus can provide microstructural insights into cell-driven remodeling of tissues.


Nanoscopic imaging of thick heterogeneous soft-matter structures in aqueous solution

Tobias F. Bartsch, Martin D. Kochanczyk, Emanuel N. Lissek, Janina R. Lange & Ernst-Ludwig Florin

Precise nanometre-scale imaging of soft structures at room temperature poses a major challenge to any type of microscopy because fast thermal fluctuations lead to significant motion blur if the position of the structure is measured with insufficient bandwidth. Moreover, precise localization is also affected by optical heterogeneities, which lead to deformations in the imaged local geometry, the severity depending on the sample and its thickness. Here we introduce quantitative thermal noise imaging, a three-dimensional scanning probe technique, as a method for imaging soft, optically heterogeneous and porous matter with submicroscopic spatial resolution in aqueous solution. By imaging both individual microtubules and collagen fibrils in a network, we demonstrate that structures can be localized with a precision of ∼10 nm and that their local dynamics can be quantified with 50 kHz bandwidth and subnanometre amplitudes. Furthermore, we show how image distortions caused by optically dense structures can be corrected for.


Bending Gold Nanorods with Light

Anastasia Babynina, Michael Fedoruk, Paul Kühler, Alexander Meledin, Markus Döblinger, and Theobald Lohmüller

V-shaped gold nanoantennas are the functional components of plasmonic metasurfaces, which are capable of manipulating light in unprecedented ways. Designing a metasurface requires the custom arrangement of individual antennas with controlled shape and orientation. Here, we show how highly crystalline gold nanorods in solution can be bent, one-by-one, into a V-shaped geometry and printed to the surface of a solid support through a combination of plasmonic heating and optical force. Significantly, we demonstrate that both the bending angle and the orientation of each rod-antenna can be adjusted independent from each other by tuning the laser intensity and polarization. This approach is applicable for the patterning of V-shaped plasmonic antennas on almost any substrate, which holds great potential for the fabrication of ultrathin optical components and devices.


Optically Evolved Assembly Formation in Laser Trapping of Polystyrene Nanoparticles at Solution Surface

Shun-Fa Wang, Tetsuhiro Kudo, Ken-ichi Yuyama, Teruki Sugiyama, and Hiroshi Masuhara

Assembling dynamics of polystyrene nanoparticles by optical trapping is studied with utilizing transmission/reflection microscopy and reflection microspectroscopy. A single nanoparticle assembly with periodic structure is formed upon the focused laser irradiation at solution surface layer and continuously grows up to a steady state within few minutes. By controlling nanoparticle and salt concentrations in the colloidal solution, the assembling behavior is obviously changed. In the high concentration of nanoparticles, the assembly formation exhibits fast growth, gives large saturation size, and leads to dense packing structure. In the presence of salt, one assembly with the elongated aggregates was generated from the focal spot and 1064 nm trapping light was scattered outwardly with directions, while a small circular assembly and symmetrical expansion of the 1064 nm light were found without salt. The present nanoparticle assembling in optical trapping is driven through multiple scattering in gathered nanoparticles and directional scattering along the elongated aggregates derived from optical association of nanoparticles, which dynamic phenomenon is called optically evolved assembling. Repetitive trapping and release processes of nanoparticles between the assembly and the surrounding solution always proceed, and the steady state at the circular assembly formed by laser trapping is determined under optical and chemical equilibrium.


Thursday, September 22, 2016

Theoretical investigation on nonlinear optical effects in laser trapping of dielectric nanoparticles with ultrafast pulsed excitation

Anita Devi and Arijit K. De

The use of low-power high-repetition-rate ultrafast pulsed excitation in stable optical trapping of dielectric nanoparticles has been demonstrated in the recent past; the high peak power of each pulse leads to instantaneous trapping of a nanoparticle with fast inertial response and the high repetition-rate ensures repetitive trapping by successive pulses However, with such high peak power pulsed excitation under a tight focusing condition, nonlinear optical effects on trapping efficiency also become significant and cannot be ignored. Thus, in addition to the above mentioned repetitive instantaneous trapping, trapping efficiency under pulsed excitation is also influenced by the optical Kerr effect, which we theoretically investigate here. Using dipole approximation we show that with an increase in laser power the radial component of the trapping potential becomes progressively more stable but the axial component is dramatically modulated due to increased Kerr nonlinearity. We justify that the relevant parameter to quantify the trapping efficiency is not the absolute depth of the highly asymmetric axial trapping potential but the height of the potential barrier along the beam propagation direction. We also discuss the optimal excitation parameters leading to the most stable dipole trap. Our results show excellent agreement with previous experiments.


Conical refraction: fundamentals and applications

Alex Turpin, Yury V. Loiko, Todor K. Kalkandjiev, Jordi Mompart

In 1832 Hamilton predicted that a collimated light beam propagating through a biaxial crystal parallel to one of its optical axes refracts as a slanted cone within the crystal and emerges as a hollow light cylinder, this optical effect being named as conical refraction (CR). The diffractive solution of CR presented by Belsky and Khapalyuk in 1978 and the corresponding re-formulation carried out by Berry in 2004 rekindled this old and almost forgotten phenomenon. In this article, we review the CR phenomenon following different approaches that allow understanding light propagation in biaxial crystals, including the case of multiple crystals in cascade. We then focus on the description of the singular properties of the CR beams, presenting some examples such as optical bottle beams and beams carrying orbital angular momentum. All these features are used to introduce some of the most appealing applications of CR in the fields of optical trapping, free-space optical communications, polarization metrology, super-resolution imaging, two-photon polymerization, and lasers.


Annular beam with segmented phase gradients

Shubo Cheng, Liang Wu and Shaohua Tao

An annular beam with a single uniform-intensity ring and multiple segments of phase gradients is proposed in this paper. Different from the conventional superposed vortices, such as the modulated optical vortices and the collinear superposition of multiple orbital angular momentum modes, the designed annular beam has a doughnut intensity distribution whose radius is independent of the phase distribution of the beam in the imaging plane. The phase distribution along the circumference of the doughnut beam can be segmented with different phase gradients. Similar to a vortex beam, the annular beam can also exert torques and rotate a trapped particle owing to the orbital angular momentum of the beam. As the beam possesses different phase gradients, the rotation velocity of the trapped particle can be varied along the circumference. The simulation and experimental results show that an annular beam with three segments of different phase gradients can rotate particles with controlled velocities. The beam has potential applications in optical trapping and optical information processing.


Guidable Thermophoretic Janus Micromotors Containing Gold Nanocolorifiers for Infrared Laser Assisted Tissue Welding

Wenping He, Johannes Frueh, Narisu Hu, Liping Liu, Meiyu Gai, Qiang He

Current wound sealing systems such as nanoparticle-based gluing of tissues allow almost immediate wound sealing. The assistance of a laser beam allows the wound sealing with higher controllability due to the collagen fiber melting which is defined by loss of tertiary protein structure and restoration upon cooling. Usually one employs dyes to paint onto the wound, if water absorption bands are absent. In case of strong bleeding or internal wounds such applications are not feasible due to low welding depth in case of water absorption bands, dyes washing off, or the dyes becoming diluted within the wound. One possible solution of these drawbacks is to use autonomously movable particles composing of biocompatible gold and magnetite nanoparticles and biocompatible polyelectrolyte complexes. In this paper a proof of principle study is presented on the utilization of thermophoretic Janus particles and capsules employed as dyes for infrared laser-assisted tissue welding. This approach proves to be efficient in sealing the wound on the mouse in vivo. The temperature measurement of single particle level proves successful photothermal heating, while the mechanical characterizations of welded liver, skin, and meat confirm mechanical restoration of the welded biological samples.


Optical Tweezers Analysis of Double-Stranded DNA Denaturation in the Presence of Urea

Chunli Zhu, and Jing Li

Urea is a kind of denaturant prone to form hydrogen bonds with the electronegative centers of the nitrogenous bases, threatening the stability of hydrogen bonds between DNA base pairs. In this paper, the stability and stiffness of DNA double helix influenced by urea are investigated at single-molecule level using optical tweezers. Experimental results show that DNA’s double helix stability and stiffness both decrease with increasing urea concentration. In addition, the re-forming of ruptured hydrogen bonds between the base pairs is blocked by urea as the tension on DNA is released.


Wednesday, September 21, 2016

Surface-enhanced Raman scattering measurement from a lipid bilayer encapsulating a single decahedral nanoparticle mediated by an optical trap

A. J. Wright, J. L. Richens, J. P. Bramble, N. Cathcart, V. Kitaev, P. O'Shea and A. J. Hudson

We present a new technique for the study of model membranes on the length-scale of a single nano-sized liposome. Silver decahedral nanoparticles have been encapsulated by a model unilamellar lipid bilayer creating nano-sized lipid vesicles. The metal core has two roles (i) increasing the polarizability of vesicles, enabling a single vesicle to be isolated and confined in an optical trap, and (ii) enhancing Raman scattering from the bilayer, via the high surface-plasmon field at the sharp vertices of the decahedral particles. Combined this has allowed us to measure a Raman fingerprint from a single vesicle of 50 nm-diameter, containing just ∼104 lipid molecules in a bilayer membrane over a surface area of <0.01 μm2, equivalent to a volume of approximately 1 zepto-litre. Raman scattering is a weak and inefficient process and previous studies have required either a substantially larger bilayer area in order to obtain a detectable signal, or the tagging of lipid molecules with a chromophore to provide an indirect probe of the bilayer. Our approach is fully label-free and bio-compatible and, in the future, it will enable much more localized studies of the heterogeneous structure of lipid bilayers and of membrane-bound components than is currently possible.


Optical gradient force assist maneuver

Alexandra B. Artusio-Glimpse, Jacob H. Wirth, and Grover A. Swartzlander

We describe an energy transfer process whereby a moving particle loses (or gains) kinetic energy upon interacting with the moving optical potential of a swept beam of light. This approach is akin to a gravitational assist maneuver for interplanetary satellite propulsion. Special consideration is given to the stopping condition. For analytical convenience, we examine the Rayleigh scattering regime, providing examples at small and large scattering angles. A 5% uncertainty in the initial particle speed and position has negligible effect on the slowing/speeding ability when the beam size is much larger than the particle.


Optical manipulation using optimal annular vortices

Rafael Paez-Lopez, Ulises Ruiz, Victor Arrizon, and Ruben Ramos-Garcia

We discuss a simple method to generate a configurable annular vortex beam (AVB) with the maximum possible peak intensity, employing a phase hologram whose transmittance is the phase of a Bessel beam. Due to its maximum intensity, the AVB provides the optimal density of the orbital angular moment. Another attribute of the generated AVB is the relatively high invariance of the intensity profile when the topological charge is changed. We demonstrate the advantages and flexibility of these AVBs for optical trapping applications.


MspA nanopore as a single-molecule tool: From sequencing to SPRNT

Andrew H. Laszlo, Ian M. Derrington, Jens H. Gundlach

Single-molecule picometer resolution nanopore tweezers (SPRNT) is a new tool for analyzing the motion of nucleic acids through molecular motors. With SPRNT, individual enzymatic motions along DNA as small as 40 pm can be resolved on sub-millisecond time scales. Additionally, SPRNT reveals an enzyme’s exact location with respect to a DNA strand’s nucleotide sequence, enabling identification of sequence-specific behaviors. SPRNT is enabled by a mutant version of the biological nanopore formed by Mycobacterium smegmatis porin A (MspA). SPRNT is strongly rooted in nanopore sequencing and therefore requires a solid understanding of basic principles of nanopore sequencing. Furthermore, SPRNT shares tools developed for nanopore sequencing and extends them to analysis of single-molecule kinetics. As such, this review begins with a brief history of our work developing the nanopore MspA for nanopore sequencing. We then describe the underlying principles of SPRNT, how it works in detail, and propose some potential future uses. We close with a comparison of SPRNT to other techniques and we present the methods that will enable others to use SPRNT.


Tuesday, September 20, 2016

Search for Screened Interactions Associated with Dark Energy below the 100 μm Length Scale

Alexander D. Rider, David C. Moore, Charles P. Blakemore, Maxime Louis, Marie Lu, and Giorgio Gratta

We present the results of a search for unknown interactions that couple to mass between an optically levitated microsphere and a gold-coated silicon cantilever. The scale and geometry of the apparatus enable a search for new forces that appear at distances below 100  μm and which would have evaded previous searches due to screening mechanisms. The data are consistent with electrostatic backgrounds and place upper limits on the strength of new interactions at <0.1  fN in the geometry tested. For the specific example of a chameleon interaction with an inverse power law potential, these results exclude matter couplings β>5.6×104 in the region of parameter space where the self-coupling Λ≳5  meV and the microspheres are not fully screened.


Quantifying Instrumental Artifacts in Folding Kinetics Measured by Single-Molecule Force Spectroscopy

Krishna Neupane, Michael T. Woodside

Force spectroscopy is commonly used to measure the kinetics of processes occurring in single biological molecules. These measurements involve attaching the molecule of interest to micron-sized or larger force probes via compliant linkers. Recent theoretical work has described how the properties of the probes and linkers can alter the observed kinetics from the intrinsic behavior of the molecule in isolation. We applied this theory to estimate the errors in measurements of folding made using optical tweezers. Errors in the folding rates arising from instrument artifacts were only ∼20% for constant-force measurements of DNA hairpins with typical choices of linker length and probe size. Measurements of transition paths using a constant trap position at high trap stiffness were also found to be in the low-artifact limit. These results indicate that typical optical trap measurements of kinetics reflect the dynamics of the molecule fairly well, and suggest practical limitations on experimental design to ensure reliable kinetic measurements.


Distinctions between dynamic characteristics of the single EG5 motor protein along neural vs. cancerous microtubules

Mitra Shojania Feizabadi, Yonggun Jun, J.N. Babu Reddy

The kinesin 5 motor contributes critically to mitosis, and is often upregulated in cancer. In vitro motility studies of kinesin 5 moving along bovine brain microtubules indicate that the motors have limited processivity. Cancer cells have abnormal mitotic behavior, so one might wonder whether the functional properties of kinesin 5 change in such a background. Because there could be multiple unknown changes in cancerous vs normal cells, we chose to address this question in a controlled in vitro environment. Specifically, through a series of parallel experiments along bovine brain vs. breast cancer microtubules, we quantified the in vitro motility characteristics of single Eg5 molecular motors along these two types of microtubules, combining the utilization of an optical trapping technique with a study of motion in the unloaded regime. The obtained values indicate that Eg5 processivity is 40% less along MCF7 microtubules, compared to that measured on bovine brain MTs. Interestingly, not all single-molecule properties are altered, as the velocity of the single motor doesn't show any significant changes on either track, though the binding time along MCF7 microtubules is almost 25% shorter. The current results, in conjunction with our previously reported outcomes of the evaluation of the Eg5's characteristics under external load, show that in transition from no-load to high-load regime, the Eg5 binding time has less sensitivity on MCF7 as compared to bovine brain MTs. This finding is intriguing, as it suggests that, potentially, groups of Eg5 motors function more effectively in the cancer background of a large ensemble, possibly contributing to faster mitosis in cancer cells.


Spinning and orbiting motion of particles in vortex beams with circular or radial polarizations

Manman Li, Shaohui Yan, Baoli Yao, Yansheng Liang, and Peng Zhang

Focusing fields of optical vortex (OV) beams with circular or radial polarizations carry both spin angular momentum (SAM) and orbital angular momentum (OAM), and can realize non-axial spinning and orbiting motion of absorptive particles. Using the T-matrix method, we evaluate the optical forces and torques exerted on micro-sized particles induced by the OV beams. Numerical results demonstrate that the particle is trapped on the circle of intensity maxima, and experiences a transverse spin torque along azimuthal direction, a longitudinal spin torque, and an orbital torque, respectively. The direction of spinning motion is not only related to the sign of topological charge of the OV beam, but also to the polarization state. However, the topological charge controls the direction of orbiting motion individually. Optically induced rotations of particles with varying sizes and absorptivity are investigated in OV beams with different topological charges and polarization states. These results may be exploited in practical optical manipulation, especially for optically induced rotations of micro-particles.


Simultaneous measurement of mass and rotation of trapped absorbing particles in air

Sudipta K. Bera, Avinash Kumar, Souvik Sil, Tushar Kanti Saha, Tanumoy Saha, and Ayan Banerjee

We trap absorbing micro-particles in air by photophoretic forces generated using a single loosely focused Gaussian trapping beam. We measure a component of the radial Brownian motion of a trapped particle cluster and determine the power spectral density, mean squared displacement, and normalized position and velocity autocorrelation functions to characterize the photophoretic body force in a quantitative fashion for the first time. The trapped particles also undergo spontaneous rotation due to the action of this force. This is evident from the spectral density that displays clear peaks at the rotation and the particles’ inertial resonance frequencies. We fit the spectral density to the well-known analytical function derived from the Langevin equation, measure the resonance and rotation frequencies, and determine the values for particle mass that we verify at different trapping laser powers with reasonable accuracy.


Monday, September 19, 2016

Waveguide-based dielectric resonance structure: a theoretical analysis to change cell–substrate separation by a repulsive optical force

Abdollah Hassanzadeh and Darya Azami

A waveguide-based dielectric resonance structure is introduced to enhance the optical pressure on a well-spread and attached cell. To calculate the change in cell–substrate separation a three-layered dielectric film, which is considered as a model for a well-spread and attached cell to its substrate, is connected to the substrate by springs. Each spring represents a single adhesion bound. The enhanced optical pressure on the sample, the changes in the cell–substrate separation distance, and strain on the cell are found. The obtained results are compared with those of both total internal reflection and interference reflection microscopes. Then, the penetration depth of the evanescent field and the enhancement factor for various modes are obtained. The results show that the enhancement factor and the optical pressure in the proposed resonance structure are 3 orders of magnitude higher than the conventional structure and the penetration depth of the evanescent wave is increased by 30 percent. We show that a measurable change in the cell–substrate distance (around 6 nm) can occur under the applied optical force. If this waveguide-based resonance structure is used in a waveguide evanescent field microscopy setup it is possible to simultaneously image and apply an effective optical pressure on cells and also to reduce the imaging time. Furthermore, there is no metal in the resonance structure to be worried about the heating and damaging biological samples.


Opto-electro-fluidics and tip coax conical surface plasmons

Touvia Miloh

The concept of electromagnetic energy enhancement and nanofocusing phenomena near the tip of a metaconical conducting tip by means of a surface plasmon-polaritons mechanism is discussed theoretically. In particular, we consider conical metallic structures with small apex angles and derive the corresponding dispersion relation under optimal (maximal field enhancement) operating conditions. It is demonstrated analytically that the aforementioned conditions can induce large dielectrophoretic forces near the conical tip, which can be harnessed for sorting and controlling nanoparticles in a manner similar to optical tweezers. Similarly, by considering Joule heating effects in the metal and heat conduction in the surrounding solute, it is shown that a considerable (dc) flow convection and mixing can be generated in the aqueous phase near the tip by such ac incited optical means (including common low-input lasers operating in the visible and near-infrared spectrum ranges). Analytic near-field expressions are also obtained for the opto-electro-thermo-induced flow and vorticity distributions in the electrolyte exhibiting a singular behavior near the rounded tip. Using a coax conical metastructure composed of two noble metals, surface-plasmon field enhancement is a technique for the optimal manipulation of dielectric and polarizable nanoparticles as well as for inducing indirect mixing in the liquid around the tip by generating microvortices.


Femtosecond scalpel-optical tweezers: efficient tool for assisted hatching and trophectoderm biopsy

D S Sitnikov, I V Ilina, Yu V Khramova, M A Filatov and M L Semenova

Ultrashort laser pulses have enabled highly precise and delicate processing of biological specimens. We present the results of using femtosecond (fs) laser pulses for dissection of zona pellucida (ZP) in mouse embryos during assisted hatching procedure and for trophectoderm biopsy as well. We studied the effects of application of fs laser radiation in the infrared (1028 nm) and visible (514 nm) wavelength ranges. Laser irradiation parameters were optimized so as not to compromise the viability of the treated embryos. Embryo biopsy was carried out in late-stage mouse preimplantation embryos. Femtosecond laser pulses were applied to detach the desired amount of trophectoderm cells from the blastocyst, while the optical tweezers trapped the cells and moved them out of the embryo. The parameters of laser radiation were optimized so as to efficiently perform embryo biopsy and preserve the viability of the treated embryos. The thermal effects can be significantly lower when fs lasers are used as compared to CW or long-pulse lasers. It is crucial when dealing with living cells or organisms.


Trapping analyte molecules in hotspots with modified free-standing silver bowtie nanostructures for SERS detection

Daren Xu, Lingxiao Liu, Fei Teng, Feifei Wu and Nan Lu

In this paper, we present a method to trap analyte molecules in hotspots by fabricating free-standing silver bowtie nanostructures with supporting bridges. The existence of supporting bridges makes more analyte molecules in hotspots, which efficiently enhance the Raman intensity. An enhancement factor of 2.4 × 108 is obtained for the structures, and a low concentration of analyte (10−10 M) can be detected. Furthermore, the relative standard deviation for Raman measurement is down to 5.91% for the structures. This method may be applied for SERS measurements.


Near-field levitated quantum optomechanics with nanodiamonds

M. L. Juan, G. Molina-Terriza, T. Volz, and O. Romero-Isart

We theoretically show that the dipole force of an ensemble of quantum emitters embedded in a dielectric nanosphere can be exploited to achieve near-field optical levitation. The key ingredient is that the polarizability from the ensemble of embedded quantum emitters can be larger than the bulk polarizability of the sphere, thereby enabling the use of repulsive optical potentials and consequently the levitation using optical near fields. In levitated cavity quantum optomechanics, this could be used to boost the single-photon coupling by combining larger polarizability to mass ratio, larger field gradients, and smaller cavity volumes while remaining in the resolved sideband regime and at room temperature. A case study is done with a nanodiamond containing a high density of silicon-vacancy color centers that is optically levitated in the evanescent field of a tapered nanofiber and coupled to a high-finesse microsphere cavity.


Friday, September 16, 2016

Relationship between the Einstein-Laub electromagnetic force and the Lorentz force on free charge

Kevin J. Webb

An electromagnetic force density expression that is consistent with a development attributed to Einstein and Laub appears to be able to describe optical force experiments done to date with homogenized media. However, a major question that has persisted for about one century relates to the apparent discrepancy with the usual interpretation of the force description due to Lorentz in magnetized media. Specifically, it had appeared that the Einstein and Laub force density incorporated only the free-space permeability in relation to the force on the electric current density. It is shown here that the Einstein and Laub force density is consistent with the Lorentz picture in the static limit. This resolves a key impediment in establishing a unified force density description for electromagnetic waves interacting with matter.


An endosomal tether undergoes an entropic collapse to bring vesicles together

David H. Murray, Marcus Jahnel, Janelle Lauer, Mario J. Avellaneda, Nicolas Brouilly, Alice Cezanne, Hernán Morales-Navarrete, Enrico D. Perini, Charles Ferguson, Andrei N. Lupas, Yannis Kalaidzidis, Robert G. Parton, Stephan W. Grill & Marino Zerial

An early step in intracellular transport is the selective recognition of a vesicle by its appropriate target membrane, a process regulated by Rab GTPases via the recruitment of tethering effectors1, 2, 3, 4. Membrane tethering confers higher selectivity and efficiency to membrane fusion than the pairing of SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) alone5, 6, 7. Here we address the mechanism whereby a tethered vesicle comes closer towards its target membrane for fusion by reconstituting an endosomal asymmetric tethering machinery consisting of the dimeric coiled-coil protein EEA1 (refs 6, 7) recruited to phosphatidylinositol 3-phosphate membranes and binding vesicles harbouring Rab5. Surprisingly, structural analysis reveals that Rab5:GTP induces an allosteric conformational change in EEA1, from extended to flexible and collapsed. Through dynamic analysis by optical tweezers, we confirm that EEA1 captures a vesicle at a distance corresponding to its extended conformation, and directly measure its flexibility and the forces induced during the tethering reaction. Expression of engineered EEA1 variants defective in the conformational change induce prominent clusters of tethered vesicles in vivo. Our results suggest a new mechanism in which Rab5 induces a change in flexibility of EEA1, generating an entropic collapse force that pulls the captured vesicle towards the target membrane to initiate docking and fusion.


Concentric Circular Grating Generated by the Patterning Trapping of Nanoparticles in an Optofluidic Chip

Hailang Dai, Zhuangqi Cao, Yuxing Wang, Honggen Li, Minghuang Sang, Wen Yuan, Fan Chen & Xianfeng Chen
Due to the field enhancement effect of the hollow-core metal-cladded optical waveguide chip, massive nanoparticles in a solvent are effectively trapped via exciting ultrahigh order modes. A concentric ring structure of the trapped nanoparticles is obtained since the excited modes are omnidirectional at small incident angle. During the process of solvent evaporation, the nanoparticles remain well trapped since the excitation condition of the optical modes is still valid, and a concentric circular grating consisting of deposited nanoparticles can be produced by this approach. Experiments via scanning electron microscopy, atomic force microscopy and diffraction of a probe laser confirmed the above hypothesis. This technique provides an alternative strategy to enable effective trapping of dielectric particles with low-intensity nonfocused illumination, and a better understanding of the correlation between the guided modes in an optical waveguide and the nanoparticles in a solvent.


Light-induced rotations of chiral birefringent microparticles in optical tweezers

M. G. Donato, A. Mazzulla, P. Pagliusi, A. Magazzù, R. J. Hernandez, C. Provenzano, P. G. Gucciardi, O. M. Maragò & G. Cipparrone

We study the rotational dynamics of solid chiral and birefringent microparticles induced by elliptically polarized laser light in optical tweezers. We find that both reflection of left circularly polarized light and residual linear retardance affect the particle dynamics. The degree of ellipticity of laser light needed to induce rotations is found. The experimental results are compared with analytical calculations of the transfer of angular moment from elliptically polarized light to chiral birefringent particles.