Monday, May 30, 2016

Force Generation by Membrane-Associated Myosin-I

Serapion Pyrpassopoulos, Göker Arpağ, Elizabeth A. Feeser, Henry Shuman, Erkan Tüzel & E. Michael Ostap

Vertebrate myosin-IC (Myo1c) is a type-1 myosin that links cell membranes to the cytoskeleton via its actin-binding motor domain and its phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2)-binding tail domain. While it is known that Myo1c bound to PtdIns(4,5)P2 in fluid-lipid bilayers can propel actin filaments in an unloaded motility assay, its ability to develop forces against external load on actin while bound to fluid bilayers has not been explored. Using optical tweezers, we measured the diffusion coefficient of single membrane-bound Myo1c molecules by force-relaxation experiments, and the ability of ensembles of membrane-bound Myo1c molecules to develop and sustain forces. To interpret our results, we developed a computational model that recapitulates the basic features of our experimental ensemble data and suggests that Myo1c ensembles can generate forces parallel to lipid bilayers, with larger forces achieved when the myosin works away from the plane of the membrane or when anchored to slowly diffusing regions.


High-resolution, hybrid optical trapping methods and their application to nucleic acid processing proteins

Yann R. Chemla

Optical tweezers have become a powerful tool to investigate nucleic-acid processing proteins at the single-molecule level. Recent advances in this technique have now enabled measurements resolving the smallest units of molecular motion, on the scale of a single base pair of DNA. In parallel, new instrumentation combining optical traps with other functionalities have been developed, incorporating mechanical manipulation along orthogonal directions or fluorescence imaging capabilities. Here, we review these technical advances, their capabilities and limitations, focusing on benchmark studies of protein-nucleic acid interactions they have enabled. We highlight recent work that combines several of these advances together and its application to nucleic-acid processing enzymes. Finally, we discuss future prospects for these exciting developments.


Comparing the energy landscapes for native folding and aggregation of PrP

Derek R. Dee & Michael T. Woodside

Protein sequences are evolved to encode generally one folded structure, out of a nearly infinite array of possible folds. Underlying this code is a funneled free energy landscape that guides folding to the native conformation. Protein misfolding and aggregation are also a manifestation of free-energy landscapes. The detailed mechanisms of these processes are poorly understood, but often involve rare, transient species and a variety of different pathways. The inherent complexity of misfolding has hampered efforts to measure aggregation pathways and the underlying energy landscape, especially using traditional methods where ensemble averaging obscures important rare and transient events. We recently studied the misfolding and aggregation of prion protein by examining two monomers tethered in close proximity as a dimer, showing how the steps leading to the formation of a stable aggregated state can be resolved in the single-molecule limit and the underlying energy landscape thereby reconstructed. This approach allows a more quantitative comparison of native folding versus misfolding, including fundamental differences in the dynamics for misfolding. By identifying key steps and interactions leading to misfolding, it should help to identify potential drug targets. Here we describe the importance of characterizing free-energy landscapes for aggregation and the challenges involved in doing so, and we discuss how single-molecule studies can help test proposed structural models for PrP aggregates.


Wednesday, May 25, 2016

Optical trapping and moving of microparticles by using asymmetrical Laguerre–Gaussian beams

Alexey A. Kovalev, Victor V. Kotlyar, and Alexey P. Porfirev

We considered a generalization of the Laguerre–Gaussian (LG) laser beam family by using a complex shift of the beam complex amplitude in Cartesian coordinates. In this case, LG-beams lose their axial symmetry. The normalized orbital angular momentum is the sum of the beam topological charge and the term which is in square dependence on the asymmetry parameter. By optical trapping and moving the polystyrene microspheres in the focus of the asymmetric LG-beam, it is proven that the velocity of the microspheres increases with increasing the asymmetry parameter and constant topological charge.


Surface plasmon-enhanced optical trapping of quantum-dot-conjugated surface molecules on neurons cultured on a plasmonic chip

Kohei Miyauchi, Keiko Tawa, Suguru N. Kudoh, Takahisa Taguchi and Chie Hosokawa

Living neurons in a complex neuronal network communicate with each other through synaptic connections. The molecular dynamics of cell surface molecules localized at synaptic terminals is essential for functional connections via synaptic plasticity in the neuronal network. Here, we demonstrate surface-plasmon-resonance-based optical trapping using a plasmonic chip toward realizing effective manipulation of molecules on the surface of neurons. Surface-plasmon-enhanced optical trapping was evaluated by the fluorescence analysis of nanoparticles suspended in water and neural cell adhesion molecules (NCAMs) labeled with quantum dots (Q-dots) on rat hippocampal neurons. The motion of nanoparticles in water and the molecular dynamics of NCAMs on neuronal cells cultured on a plasmonic chip were constrained at the laser focus more effectively than those on a glass substrate because of the surface plasmon resonance effect.


Near-field probing of Bloch surface waves in a dielectric multilayer using photonic force microscopy

Daniil A. Shilkin, Evgeny V. Lyubin, Irina V. Soboleva, and Andrey A. Fedyanin

The potential of photonic force microscopy (PFM) for probing the optical near-field in the vicinity of a dielectric multilayer is demonstrated. An experimental study of Bloch surface waves (BSWs) using PFM is described in detail. The applied technique is based on measuring the BSW-induced gradient force acting on a probe particle combined with precise control of the distance between the particle and the multilayer surface. The BSW-induced potential profile measured using PFM is presented. The force interaction between the probe and the BSW evanescent field is numerically studied. The results indicate that a polystyrene particle with a diameter of 1 μm does not significantly perturb the BSW field and can be used to probe the optical near-field intensity in an elegant, noninvasive manner.


Two-Photon Fluorescence Tracking of Colloidal Clusters

Debjit Roy, Dipankar Mondal, Debabrata Goswami

In situ dynamics of colloidal cluster formation from nanoparticles is yet to be addressed. Using two-photon fluorescence (TPF) that has been amply used for single particle tracking, we demonstrate in situ measurement of effective three-dimensional optical trap stiffness of nanoparticles and their aggregates without using any position sensitive detector. Optical trap stiffness is an essential measure of the strength of an optical trap. TPF is a zero-background detection scheme and has excellent signal-to-noise-ratio, which can be easily extended to study the formation of colloidal cluster of nanospheres in the optical trapping regime. TPF tracking can successfully distinguish colloidal cluster from its monomer.


Tuesday, May 24, 2016

A Comprehensive Review of Optical Stretcher for Cell Mechanical Characterization at Single-Cell Level

Tie Yang, Francesca Bragheri and Paolo Minzioni

This paper presents a comprehensive review of the development of the optical stretcher, a powerful optofluidic device for single cell mechanical study by using optical force induced cell stretching. The different techniques and the different materials for the fabrication of the optical stretcher are first summarized. A short description of the optical-stretching mechanism is then given, highlighting the optical force calculation and the cell optical deformability characterization. Subsequently, the implementations of the optical stretcher in various cell-mechanics studies are shown on different types of cells. Afterwards, two new advancements on optical stretcher applications are also introduced: the active cell sorting based on cell mechanical characterization and the temperature effect on cell stretching measurement from laser-induced heating. Two examples of new functionalities developed with the optical stretcher are also included. Finally, the current major limitation and the future development possibilities are discussed.


Graded-index optical dimer formed by optical force

Alireza Akbarzadeh, Thomas Koschny, Maria Kafesaki, Eleftherios N. Economou, and Costas M. Soukoulis

We propose an optical dimer formed from two spherical lenses bound by the pressure that light exerts on matter. With the help of the method of force tracing, we find the required graded-index profiles of the lenses for the existence of the dimer. We study the dynamics of the opto-mechanical interaction of lenses under the illumination of collimated light beams and quantitatively validate the performance of proposed dimer. We also examine the stability of dimer due to the lateral misalignments and we show how restoring forces bring the dimer into lateral equilibrium. The dimer can be employed in various practical applications such as optical manipulation, sensing and imaging.


Improved calibration of the nonlinear regime of a single-beam gradient optical trap

Jamianne C. Wilcox, Benjamin J. Lopez, Otger Campàs, and Megan T. Valentine

We report an improved method for calibrating the nonlinear region of a single-beam gradient optical trap. Through analysis of the position fluctuations of a trapped object that is displaced from the trap center by controlled flow we measure the local trap stiffness in both the linear and nonlinear regimes without knowledge of the magnitude of the applied external forces. This approach requires only knowledge of the system temperature, and is especially useful for measurements involving trapped objects of unknown size, or objects in a fluid of unknown viscosity.


Lateral shearing optical gradient force in coupled nanobeam photonic crystal cavities

Han Du, Xingwang Zhang, Jie Deng, Yunshan Zhao, Fook Siong Chau and Guangya Zhou

We report the experimental observation of lateral shearing optical gradient forces in nanoelectromechanical systems(NEMS) controlled dual-coupled photonic crystal(PhC) nanobeam cavities. With an on-chip integrated NEMS actuator, the coupled cavities can be mechanically reconfigured in the lateral direction while maintaining a constant coupling gap. Shearing optical gradient forces are generated when the two cavity centers are laterally displaced. In our experiments, positive and negative lateral shearing optical forces of 0.42 nN and 0.29 nN are observed with different pumping modes. This study may broaden the potential applications of the optical gradient force in nanophotonic devices and benefit the future nanooptoelectromechanical systems.


Monday, May 23, 2016

Formation of stable cell–cell contact without a solid/gel scaffold: Non-invasive manipulation by laser under depletion interaction with a polymer

Shu Hashimoto, Aoi Yoshida, Taeko Ohta, Hiroaki Taniguchi, Koichiro Sadakane, Kenichi Yoshikawa

We report a novel method for constructing a stable three-dimensional cellular assembly in the absence of a solid or gel scaffold. A targeted cell was transferred to another cell, and the two were kept in contact for a few minutes by optical manipulation in an aqueous medium containing a hydrophilic polymer. Interestingly, this cell–cell adhesion was maintained even after elimination of the polymer. We discuss the mechanism of the formation of stable multi-cellular adhesion in terms of spontaneous rearrangement of the components embedded in the pair of facing membranes.


Graphene-based multilayer resonance structure to enhance the optical pressure on a Mie particle

Abdollah Hassanzadeh; Mohammadbagher Mohammadnezhad

We theoretically investigate the optical force exerted on a Mie dielectric particle in the evanescent field of a graphene-based resonance multilayer structure using the arbitrary beam theory and the theory of multilayer films. The resonance structure consists of several thin films including a dielectric film (MgF2MgF2), a metal film (silver or gold), and several graphene layers which are located on a prism base. The effects of the metal film thickness and the number of graphene layers on the optical force are numerically investigated. The thickness of the metal layer and the number of graphene layers are optimized to reach the highest optical force. The numerical results show that an optimized composition of graphene and gold leads to a higher optical force compared to that of the graphene and silver. The optical force was enhanced resonantly by four orders of magnitude for the resonance structure containing graphene and a gold film and by three orders of magnitude for the structure containing graphene and a silver film compared to other similar resonance structures. We hope that the results presented in this paper can provide an excellent means of improving the optical manipulation of particles and enable the provision of effective optical tweezers, micromotors, and microaccelelators.


Defining Single Molecular Forces Required for Notch Activation Using Nano Yoyo

Farhan Chowdhury, Isaac T. S. Li, Thuy T. M. Ngo, Benjamin J. Leslie, Byoung Choul Kim, Joshua E. Sokoloski, Elizabeth Weiland, Xuefeng Wang, Yann R. Chemla, Timothy M. Lohman, and Taekjip Ha

Notch signaling, involved in development and tissue homeostasis, is activated at the cell–cell interface through ligand–receptor interactions. Previous studies have implicated mechanical forces in the activation of Notch receptor upon binding to its ligand. Here we aimed to determine the single molecular force required for Notch activation by developing a novel low tension gauge tether (LTGT). LTGT utilizes the low unbinding force between single-stranded DNA (ssDNA) and Escherichia coli ssDNA binding protein (SSB) (∼4 pN dissociation force at 500 nm/s pulling rate). The ssDNA wraps around SSB and, upon application of force, unspools from SSB, much like the unspooling of a yoyo. One end of this nano yoyo is attached to the surface though SSB, while the other end presents a ligand. A Notch receptor, upon binding to its ligand, is believed to undergo force-induced conformational changes required for activating downstream signaling. If the required force for such activation is larger than 4 pN, ssDNA will unspool from SSB, and downstream signaling will not be activated. Using these LTGTs, in combination with the previously reported TGTs that rupture double-stranded DNA at defined forces, we demonstrate that Notch activation requires forces between 4 and 12 pN, assuming an in vivo loading rate of 60 pN/s. Taken together, our study provides a direct link between single-molecular forces and Notch activation.


Trapping and Detection of Nanoparticles and Cells Using a Parallel Photonic Nanojet Array

Yuchao Li, Hongbao Xin, Xiaoshuai Liu, Yao Zhang, Hongxiang Lei, and Baojun Li

In advanced nanoscience, there is a strong desire to trap and detect nanoscale objects with high-throughput, single-nanoparticle resolution and high selectivity. Although emerging optical methods have enabled the selective trapping and detection of multiple micrometer-sized objects, it remains a great challenge to extend this functionality to the nanoscale. Here, we report an approach to trap and detect nanoparticles and subwavelength cells at low optical power using a parallel photonic nanojet array produced by assembling microlenses on an optical fiber probe. Benefiting from the subwavelength confinement of the photonic nanojets, tens to hundreds of nanotraps were formed in three dimensions. Backscattering signals were detected in real time with single-nanoparticle resolution and enhancement factors of 103–104. Selective trapping of nanoparticles and cells from a particle mixture or human blood solution was demonstrated using the nanojet array. The developed nanojet array is potentially a powerful tool for nanoparticle assembly, biosensing, single-cell analysis, and optical sorting.


Pushing nanoparticles with light — A femtonewton resolved measurement of optical scattering forces

C. Zensen, N. Villadsen, F. Winterer, S. R. Keiding and T. Lohmüller

Optomechanical manipulation of plasmonic nanoparticles is an area of current interest, both fundamental and applied. However, no experimental method is available to determine the forward-directed scattering force that dominates for incident light of a wavelength close to the plasmon resonance. Here, we demonstrate how the scattering force acting on a single gold nanoparticle in solution can be measured. An optically trapped 80 nm particle was repetitively pushed from the side with laser light resonant to the particle plasmon frequency. A lock-in analysis of the particle movement provides a measured value for the scattering force. We obtain a resolution of less than 3 femtonewtons which is an order of magnitude smaller than any measurement of switchable forces performed on nanoparticles in solution with single beam optical tweezers to date. We compared the results of the force measurement with Mie simulations of the optical scattering force on a gold nanoparticle and found good agreement between experiment and theory within a few fN.


Saturday, May 21, 2016

Plasmon optical trapping using silicon nitride trench waveguides

Qiancheng Zhao, Caner Guclu, Yuewang Huang, Filippo Capolino, Regina Ragan, and Ozdal Boyraz

We theoretically demonstrate optical trapping using a silicon nitride (Si3N4) trench waveguide on which bow-tie plasmonic nanoantennas are employed for enhancing optical forces. The electric field tailing away from the waveguide is transformed and then enhanced by the plasmonic nanoantennas deposited on the waveguide surface. We show that, with gold bow-tie nanoantennas, the waveguide system exhibits outstanding trapping capability on a 10 nm radius polystyrene nanoparticle, due to a 60-fold electric field enhancement in the proximity of the nanoantenna gap. This enhancement causes a boost of the optical trapping force by 3 orders of magnitude. The gradient force in the vertical direction is also calculated semi-analytically by using a dipole approximation of a scattering polystyrene nanosphere, and the analytical solution well matches the full-wave simulations. Mode polarization effects are discussed in this paper as a way to switch trapping. These investigations indicate that the patterned Si3N4 trench waveguide is suitable for optical trapping and nanoparticle sensing applications.


Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models

Lu Zhang, Fátima Pardo-Avila, Ilona Christy Unarta, Peter Pak-Hang Cheung, Guo Wang, Dong Wang, and Xuhui Huang

RNA polymerase II (Pol II) is an essential enzyme that catalyzes transcription with high efficiency and fidelity in eukaryotic cells. During transcription elongation, Pol II catalyzes the nucleotide addition cycle (NAC) to synthesize mRNA using DNA as the template. The transitions between the states of the NAC require conformational changes of both the protein and nucleotides. Although X-ray structures are available for most of these states, the dynamics of the transitions between states are largely unknown. Molecular dynamics (MD) simulations can predict structure-based molecular details and shed light on the mechanisms of these dynamic transitions. However, the employment of MD simulations on a macromolecule (tens to hundreds of nanoseconds) such as Pol II is challenging due to the difficulty of reaching biologically relevant timescales (tens of microseconds or even longer). For this challenge to be overcome, kinetic network models (KNMs), such as Markov State Models (MSMs), have become a popular approach to access long-timescale conformational changes using many short MD simulations.
We describe here our application of KNMs to characterize the molecular mechanisms of the NAC of Pol II. First, we introduce the general background of MSMs and further explain procedures for the construction and validation of MSMs by providing some technical details. Next, we review our previous studies in which we applied MSMs to investigate the individual steps of the NAC, including translocation and pyrophosphate ion release. In particular, we describe in detail how we prepared the initial conformations of Pol II elongation complex, performed MD simulations, extracted MD conformations to construct MSMs, and further validated them. We also summarize our major findings on molecular mechanisms of Pol II elongation based on these MSMs. In addition, we have included discussions regarding various key points and challenges for applications of MSMs to systems as large as the Pol II elongation complex. Finally, to study the overall NAC, we combine the individual steps of the NAC into a five-state KNM based on a nonbranched Brownian ratchet scheme to explain the single-molecule optical tweezers experimental data. The studies complement experimental observations and provide molecular mechanisms for the transcription elongation cycle. In the long term, incorporation of sequence-dependent kinetic parameters into KNMs has great potential for identifying error-prone sequences and predicting transcription dynamics in genome-wide transcriptomes.


Plasmon enhanced optical tweezers with gold-coated black silicon

D. G. Kotsifaki, M. Kandyla & P. G. Lagoudakis

Plasmonic optical tweezers are a ubiquitous tool for the precise manipulation of nanoparticles and biomolecules at low photon flux, while femtosecond-laser optical tweezers can probe the nonlinear optical properties of the trapped species with applications in biological diagnostics. In order to adopt plasmonic optical tweezers in real-world applications, it is essential to develop large-scale fabrication processes without compromising the trapping efficiency. Here, we develop a novel platform for continuous wave (CW) and femtosecond plasmonic optical tweezers, based on gold-coated black silicon. In contrast with traditional lithographic methods, the fabrication method relies on simple, single-step, maskless tabletop laser processing of silicon in water that facilitates scalability. Gold-coated black silicon supports repeatable trapping efficiencies comparable to the highest ones reported to date. From a more fundamental aspect, a plasmon-mediated efficiency enhancement is a resonant effect, and therefore, dependent on the wavelength of the trapping beam. Surprisingly, a wavelength characterization of plasmon-enhanced trapping efficiencies has evaded the literature. Here, we exploit the repeatability of the recorded trapping efficiency, offered by the gold-coated black silicon platform, and perform a wavelength-dependent characterization of the trapping process, revealing the resonant character of the trapping efficiency maxima. Gold-coated black silicon is a promising platform for large-scale parallel trapping applications that will broaden the range of optical manipulation in nanoengineering, biology, and the study of collective biophotonic effects.


Comparative study of optical levitation traps: focused Bessel beam versus Gaussian beams

Yareni A. Ayala, Alejandro V. Arzola, and Karen Volke-Sepúlveda

In optical levitation traps, a light beam propagating upward is focused with a relatively low numerical aperture (NA), producing a large scattering force along the propagation direction, which is balanced by the effective weight of a particle. Here, we present a detailed study of four levitation traps obtained when the trapping beam is a fundamental Gaussian mode focused with different NA, in comparison with a levitation trap obtained with a zero-order Bessel beam focused through a lens with NA=0.40. A theoretical analysis for the optical field and trapping forces along the lateral and axial directions is presented for all the traps and contrasted with experimental results. We show that the focused Bessel trap offers highly superior capabilities for manipulation of individual glass beads in three dimensions, along with other advantages in comparison with standard optical tweezers, such as an extended working distance, larger field of view, and lower spherical aberration.


Tuesday, May 17, 2016

Light-Driven Delivery and Release of Materials Using Liquid Marbles

Maxime Paven, Hiroyuki Mayama, Takafumi Sekido, Hans-Jürgen Butt, Yoshinobu Nakamura, Syuji Fujii

Remote control of the locomotion of small objects is a challenge in itself and may also allow for the stimuli control of entire systems. Here, it is described how encapsulated liquids, referred to as liquid marbles, can be moved on a water surface with a simple near-infrared laser or sunlight. Using light rather than pH or temperature as an external stimulus allows for the control of the position, area, timing, direction, and velocity of delivery. This approach makes it possible to not only transport the materials encapsulated within the liquid marble but also to release them at a specific place and time, as controlled by external stimuli. Furthermore, it is shown that liquid marbles can work as light-driven towing engines to push or pull objects. Being able to remotely transport and push/pull the small objects by light and control the release of active substances on demand should open up a wide field of conceivable applications.


Tuning the stiffness asymmetry of optical tweezers via polarization control

Jinmyoung So, Jai-Min Choi

We report an experimental demonstration of tailoring the landscape of the optical potential by using the polarization state of a trap laser beam as a tuning knob. Two groups of polystyrene spheres, i.e., 300 nm and 1 μm, are optically trapped individually to investigate the effect of the intrinsic and a strongly-modified optical field distribution on the resulting trap stiffness, respectively. The angular variations of the orthogonal pair of stiffnesses, k x and k y , with the polarization state of the trap laser beam were systematically analyzed, and the results show that polarization control could provide a wide tuning range of trap-stiffness asymmetry (s T = 1− k x /k y ). The implication of asymmetry control of the optical potential is briefly discussed.


Using Brownian motion to measure shape asymmetry in mesoscopic matter using optical tweezers

Basudev Roy, Argha Mondal, Sudipta K Bera and Ayan Banerjee

We propose a new method for quantifying shape asymmetry in the mesoscopic scale. The method takes advantage of the intrinsic coupling between rotational and translational Brownian motion (RBM and TBM, respectively) which happens in the case of asymmetric particles. We determine the coupling by measuring different correlation functions of the RBM and TBM for single, morphologically different, weakly-trapped red blood cells in optical tweezers. The cells have different degrees of asymmetry that are controllably produced by varying the hypertonicity of their aqueous environment. We demonstrate a clear difference in the nature of the correlation functions both qualitatively and quantitatively for three types of cells having a varying degree of asymmetry. This method can have a variety of applications ranging from early stage disease diagnosis to quality control in microfabrication.


Characterization of the near-field and convectional transport behavior of micro and nanoparticles in nanoscale plasmonic optical lattices

Tsang-Po Yang, Gilad Yossifon and Ya-Tang Yang

Here, we report the characterization of the transport of micro- and nanospheres in a simple two-dimensional square nanoscale plasmonic optical lattice. The optical potential was created by exciting plasmon resonance by way of illuminating an array of gold nanodiscs with a loosely focused Gaussian beam. This optical potential produced both in-lattice particle transport behavior, which was due to near-field optical gradient forces, and high-velocity (∼μm/s) out-of-lattice particle transport. As a comparison, the natural convection velocity field from a delocalized temperature profile produced by the photothermal heating of the nanoplasmonic array was computed in numerical simulations. This work elucidates the role of photothermal effects on micro- and nanoparticle transport in plasmonic optical lattices.


Friday, May 13, 2016

Regulation of DNA Translocation Efficiency within the Chromatin Remodeler RSC/Sth1 Potentiates Nucleosome Sliding and Ejection

Cedric R. Clapier, Margaret M. Kasten, Timothy J. Parnell, Ramya Viswanathan, Heather Szerlong, George Sirinakis, Yongli Zhang, Bradley R. Cairns

The RSC chromatin remodeler slides and ejects nucleosomes, utilizing a catalytic subunit (Sth1) with DNA translocation activity, which can pump DNA around the nucleosome. A central question is whether and how DNA translocation is regulated to achieve sliding versus ejection. Here, we report the regulation of DNA translocation efficiency by two domains residing on Sth1 (Post-HSA and Protrusion 1) and by actin-related proteins (ARPs) that bind Sth1. ARPs facilitated sliding and ejection by improving “coupling”—the amount of DNA translocation by Sth1 relative to ATP hydrolysis. We also identified and characterized Protrusion 1 mutations that promote “coupling,” and Post-HSA mutations that improve ATP hydrolysis; notably, the strongest mutations conferred efficient nucleosome ejection without ARPs. Taken together, sliding-to-ejection involves a continuum of DNA translocation efficiency, consistent with higher magnitudes of ATPase and coupling activities (involving ARPs and Sth1 domains), enabling the simultaneous rupture of multiple histone-DNA contacts facilitating ejection.


A TOG Protein Confers Tension Sensitivity to Kinetochore-Microtubule Attachments

Matthew P. Miller, Charles L. Asbury, Sue Biggins

The development and survival of all organisms depends on equal partitioning of their genomes during cell division. Accurate chromosome segregation requires selective stabilization of kinetochore-microtubule attachments that come under tension due to opposing pulling forces exerted on sister kinetochores by dynamic microtubule tips. Here, we show that the XMAP215 family member, Stu2, makes a major contribution to kinetochore-microtubule coupling. Stu2 and its human ortholog, ch-TOG, exhibit a conserved interaction with the Ndc80 kinetochore complex that strengthens its attachment to microtubule tips. Strikingly, Stu2 can either stabilize or destabilize kinetochore attachments, depending on the level of kinetochore tension and whether the microtubule tip is assembling or disassembling. These dichotomous effects of Stu2 are independent of its previously studied regulation of microtubule dynamics. Altogether, our results demonstrate how a kinetochore-associated factor can confer opposing, tension-dependent effects to selectively stabilize tension-bearing attachments, providing mechanistic insight into the basis for accuracy during chromosome segregation.


Impurity-tuned non-equilibrium phase transition in a bacterial carpet

Yi-Teng Hsiao, Kuan-Ting Wu, Nariya Uchida and Wei-Yen Woon
The effects of impurity on the non-equilibrium phase transition in Vibrio alginolyticus bacterial carpets are investigated through a position-sensitive-diode implemented optical tweezers-microsphere assay. The collective flow increases abruptly as we increase the rotation rate of flagella via Na+ concentration. The effects of impurities on the transition behavior are examined by mixing cells of a wild type strain (VIO5) with cells of a mutant strain (NMB136) in different swimming patterns. For dilute impurities, the transition point is shifted toward higher Na+ concentration. Increasing the impurities' ratio to over 0.25 leads to a significant drop in the collective force, suggesting a partial orientational order with a smaller correlation length.


Cancellation of non-conservative scattering forces in optical traps by counter-propagating beams: erratum

Shawn Divitt, Loïc Rondin, and Lukas Novotny

In a previous Letter [Opt. Lett. 40, 1900 (2015) [CrossRef] ], we asserted that two counter-propagating beams must be polarized with opposite handedness to cancel scattering forces. A more careful calculation shows that this is not the case. The correct condition is achieved by beams with the same handedness, as derived in this Erratum.


Sensitive in situ nanothermometer using femtosecond optical tweezers

Dipankar Mondal; Debabrata Goswami

We report the rise in temperature in various liquid media adjacent to a trapped bead. A nonheating laser at 780 nm has been used to optically trap a 500-nm radius polystyrene bead, while a simultaneous irradiation with a copropagating 1560-nm high-repetition-rate femtosecond laser led to temperature rise in various trapping media. Vibrational combination band of the hydroxyl group in the trapping media resulted in high absorption of 1560-nm laser. This, in turn, gave us control over the trapping media temperature at the focus of the optical trap.


Tuesday, May 10, 2016

Motility, Force Generation, and Energy Consumption of Unicellular Parasites

Axel Hochstetter, Thomas Pfohl

Motility is a key factor for pathogenicity of unicellular parasites, enabling them to infiltrate and evade host cells, and perform several of their life-cycle events. State-of-the-art methods of motility analysis rely on a combination of optical tweezers with high-resolution microscopy and microfluidics. With this technology, propulsion forces, energies, and power generation can be determined so as to shed light on the motion mechanisms, chemotactic behavior, and specific survival strategies of unicellular parasites. With these new tools in hand, we can elucidate the mechanisms of motility and force generation of unicellular parasites, and identify ways to manipulate and eventually inhibit them.


Gap mode induced laser trapping of silver nanoparticles on thiophenol-covered silver substrates

Chiaki Iida, Keitaro Akai, Junichi Murakami, Masayuki Futamata
Silver nanoparticles (AgNPs) with radius of ∼20 nm were optically trapped and immobilized on thiophenol (TP)-covered Ag films under a gap mode resonance with extremely weak power density of ∼1 μW/μm2 at 532 nm. Intensity of Raman scattering from TP markedly increased with the accumulation of AgNPs. Trapping efficiency of AgNPs for p-polarization was 2-4 times higher than that for s-polarization. The observed optical trapping and immobilization were theoretically rationalized using a dipole-dipole coupling under a gap mode and van der Waals interaction between AgNPs and Ag films, which facilitate to fabricate versatile substrates for surface enhanced Raman scattering.


Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging

Nicholas Keller, Shelley Grimes, Paul J. Jardine & Douglas E. Smith

In many viruses, molecular motors forcibly pack single DNA molecules to near-crystalline density into ~50–100 nm prohead shells. Unexpectedly, we found that packaging frequently stalls in conditions that induce net attractive DNA–DNA interactions. Here, we present findings suggesting that this stalling occurs because the DNA undergoes a nonequilibrium jamming transition analogous to that observed in many soft-matter systems, such as colloidal and granular systems. Experiments in which conditions are changed during packaging to switch DNA–DNA interactions between purely repulsive and net attractive reveal strongly history-dependent dynamics. An abrupt deceleration is usually observed before stalling, indicating that a transition in DNA conformation causes an abrupt increase in resistance. Our findings suggest that the concept of jamming can be extended to a single polymer molecule. However, compared with macroscopic samples of colloidal particles5 we find that single DNA molecules jam over a much larger range of densities. We attribute this difference to the nanoscale system size, consistent with theoretical predictions for jamming of attractive athermal particles.


Wednesday, May 4, 2016

The equation of motion of the photon in an optical medium

V.P. Torchigin, A.V. Torchigin

We show that the equation of the photon motion coincides with the eikonal equation on the assumption that the photon momentum in an optical medium increases by n times compared with that in free space and the density force applied to the photon is determined by the density force derived by the Maxwell for the force in the dielectric located in an electrical field.


Charge renormalization in nominally apolar colloidal dispersions

Daniel J. Evans, Andrew D. Hollingsworth, and David G. Grier

We present high-resolution measurements of the pair interactions between dielectric spheres dispersed in a fluid medium with a low dielectric constant. Despite the absence of charge control agents or added organic salts, these measurements reveal strong and long-ranged repulsions consistent with substantial charges on the particles whose interactions are screened by trace concentrations of mobile ions in solution. The dependence of the estimated charge on the particles' radii is consistent with charge renormalization theory and, thus, offers insights into the charging mechanism in this interesting class of model systems. The measurement technique, based on optical-tweezer manipulation and artifact-free particle tracking, makes use of optimal statistical methods to reduce measurement errors to the femtonewton frontier while covering an extremely wide range of interaction energies.


Quantitative Correlation between Infectivity and Gp120 Density on HIV-1 Virions Revealed by Optical Trapping Virometry

Michael C. DeSantis, Jin H. Kim, Hanna Song, Per Johan Klasse and Wei Cheng

The envelope glycoprotein (Env) gp120/gp41 is required for HIV-1 infection of host cells. Although in general it has been perceived that more Env gives rise to higher infectivity, the precise quantitative dependence of HIV-1 virion infectivity on Env density has remained unknown. Here we have developed a method to examine this dependence. This method involves (1) production of a set of single-cycle HIV-1 virions with varied density of Env on their surface; (2) site-specific labeling of Env-specific antibody Fab with a fluorophore at high efficiency, and (3) optical trapping virometry to measure the number of gp120 molecules on individual HIV-1 virions. The resulting gp120 density per virion is then correlated with the infectivity of the virions measured in cell culture. In the presence of DEAE-dextran, the polycation known to enhance HIV-1 infectivity in cell culture, virion infectivity follows gp120 density as a sigmoidal dependence and reaches an apparent plateau. This quantitative dependence can be described by a Hill equation, with Hill coefficient of 2.4 ± 0.6. In contrast, in the absence of DEAE-dextran, virion infectivity increases monotonically with gp120 density and no saturation is observed under the experimental conditions. These results provide the first quantitative evidence that Env trimers cooperate on the virion surface to mediate productive infection by HIV-1. Moreover, as a result of the low number of Env trimers on individual virions, the number of additional Env trimers per virion that is required for the optimal infectivity will depend on the inclusion of facilitating agents during infection.


Graphene-based plasmonic tweezers

Jung-Dae Kim, Yong-Gu Lee

Conventional plasmonic tweezers with the ability to attract and immobilize nearby sub-diffraction limit sized particles can only enhance the trapping efficiency by changing the shape of the metal nanostructures. There are several problems with conventional plasmonic tweezers. First, trapped particles can easily escape from the trap by disturbances coming from the heat absorption of the metallic surfaces. These disturbances prevent prolonged observation of the trapped particles. Second, observation of the particles becomes a challenge because the opaqueness of the metal blocks the illumination pathways. These problems can be solved by using graphene, which has high transmittance and thermal conductivity. The carrier density of the graphene is tuned by externally controlling the Fermi level through the gate voltage. Tuning the carrier density alters the local field enhancement factor far beyond the capabilities provided by other metal-based plasmonic structures. In this paper, we have shown that particles can be trapped by graphene nanoholes with larger forces than gold nanoholes. The trapping forces on gold and graphene nanoholes were compared to illustrate the benefit of graphene nanoholes. Furthermore, various trapping modes of a particle under various geometries and configurations of graphene nanoholes is discussed.


Tuesday, May 3, 2016

Surface plasmon polariton scattering by subwavelength silicon wires

Mehdi Shafiei Aporvari, Ahmad Shafiei Aporvari, and Fardin Kheirandish

Surface plasmon polariton scattering from 2D subwavelength silicon wires is investigated using the finite-difference time-domain method. It is shown that coupling an incident surface plasmon polariton to intercavity modes of the particle can dramatically change transmitted fields and plasmon-induced forces. In particular, both transmission and optical forces are highly sensitive to the particle size that is related to the excitation of whispering gallery modes or standing wave modes depending on the particle shape and size. These features might have potential sensing applications.


Active multi-point microrheology of cytoskeletal networks

Tobias Paust, Tobias Neckernuss, Lina Katinka Mertens, Ines Martin, Michael Beil, Paul Walther, Thomas Schimmel and Othmar Marti

Active microrheology is a valuable tool to determine viscoelastic properties of polymer networks. Observing the response of the beads to the excitation of a reference leads to dynamic and morphological information of the material. In this work we present an expansion of the well-known active two-point microrheology. By measuring the response of multiple particles in a viscoelastic medium in response to the excitation of a reference particle, we are able to determine the force propagation in the polymer network. For this purpose a lock-in technique is established that allows for extraction of the periodical motion of embedded beads. To exert a sinusoidal motion onto the reference bead an optical tweezers setup in combination with a microscope is used to investigate the motion of the response beads. From the lock-in data the so called transfer tensor can be calculated, which is a direct measure for the ability of the network to transmit mechanical forces. We also take a closer look at the influence of noise on lock-in measurements and state some simple rules for improving the signal-to-noise ratio.


Single-Molecule Chemo-Mechanical Spectroscopy Provides Structural Identity of Folding Intermediates

Hesam N. Motlagh, Dmitri Toptygin, Christian M. Kaiser, Vincent J. Hilser

Single-molecule force spectroscopy has emerged as a powerful tool for studying the folding of biological macromolecules. Mechanical manipulation has revealed a wealth of mechanistic information on transient and intermediate states. To date, the majority of state assignment of intermediates has relied on empirical demarcation. However, performing such experiments in the presence of different osmolytes provides an alternative approach that reports on the structural properties of intermediates. Here, we analyze the folding and unfolding of T4 lysozyme with optical tweezers under a chemo-mechanical perturbation by adding osmolytes. We find that two unrelated protective osmolytes, sorbitol and trimethylamine-n-oxide, function by marginally decelerating unfolding rates and specifically modulating early events in the folding process, stabilizing formation of an on-pathway intermediate. The chemo-mechanical perturbation provides access to two independent metrics of the relevant states during folding trajectories, the contour length, and the solvent-accessible surface area. We demonstrate that the dependence of the population of the intermediate in different osmolytes, in conjunction with its measured contour length, provides the ability to discriminate between potential structural models of intermediate states. Our study represents a general strategy that may be employed in the structural modeling of equilibrium intermediate states observed in single-molecule experiments.


Dissecting the Dynamic Pathways of Stereoselective DNA Threading Intercalation

Ali A. Almaqwashi, Johanna Andersson, Per Lincoln, Ioulia Rouzina, Fredrik Westerlund, Mark C. Williams

DNA intercalators that have high affinity and slow kinetics are developed for potential DNA-targeted therapeutics. Although many natural intercalators contain multiple chiral subunits, only intercalators with a single chiral unit have been quantitatively probed. Dumbbell-shaped DNA threading intercalators represent the next order of structural complexity relative to simple intercalators, and can provide significant insights into the stereoselectivity of DNA-ligand intercalation. We investigated DNA threading intercalation by binuclear ruthenium complex [μ-dppzip(phen)4Ru2]4+ (Piz). Four Piz stereoisomers are defined by the chirality of the intercalating subunit (Ru(phen)2dppz) and the distal subunit (Ru(phen)2ip), respectively, each of which can be either right-handed (Δ) or left-handed (Λ). We used optical tweezers to measure single DNA molecule elongation due to threading intercalation, revealing force-dependent DNA intercalation rates and equilibrium dissociation constants. The force spectroscopy analysis provided the zero-force DNA binding affinity, the equilibrium DNA-ligand elongation Δxeq, and the dynamic DNA structural deformations during ligand association xon and dissociation xoff. We found that Piz stereoisomers exhibit over 20-fold differences in DNA binding affinity, from a Kd of 27 ± 3 nM for (Δ,Λ)-Piz to a Kd of 622 ± 55 nM for (Λ,Δ)-Piz. The striking affinity decrease is correlated with increasing Δxeq from 0.30 ± 0.02 to 0.48 ± 0.02 nm and xon from 0.25 ± 0.01 to 0.46 ± 0.02 nm, but limited xoff changes. Notably, the affinity and threading kinetics is 10-fold enhanced for right-handed intercalating subunits, and 2- to 5-fold enhanced for left-handed distal subunits. These findings demonstrate sterically dispersed transition pathways and robust DNA structural recognition of chiral intercalators, which are critical for optimizing DNA binding affinity and kinetics.


Tractor beams in the Rayleigh limit

Aaron Yevick, David B. Ruffner, and David G. Grier

A tractor beam is a traveling wave that transports illuminated objects back to its source, opposite to the wave's direction of propagation, along its entire length. The requisite retrograde force arises when an object scatters the wave's momentum density downstream into the direction of propagation and then recoils upstream by conservation of momentum. Achieving this condition imposes constraints on the structure of the wave, which we elucidate in the Rayleigh limit, when the wavelength exceeds the size of the object. Continuously propagation-invariant modes such as Bessel beams do not satisfy these conditions at dipole order in the multipole expansion and so cannot serve as general-purpose long-ranged tractor beams. Modes with discrete propagation invariance, however, can act as first-order tractor beams. We demonstrate this by introducing a class of minimal solenoidal waves together with a set of design criteria that distinguish tractor beams that pull objects from repulsor beams that push them.


Monday, May 2, 2016

Direct measurements of the extraordinary optical momentum and transverse spin-dependent force using a nano-cantilever

M. Antognozzi, C. R. Bermingham, R. L. Harniman, S. Simpson, J. Senior, R. Hayward, H. Hoerber, M. R. Dennis, A. Y. Bekshaev, K. Y. Bliokh & F. Nori

Radiation pressure is associated with the momentum of light, and it plays a crucial role in a variety of physical systems. It is usually assumed that both the optical momentum and the radiation-pressure force are naturally aligned with the propagation direction of light, given by its wavevector. Here we report the direct observation of an extraordinary optical momentum and force directed perpendicular to the wavevector, and proportional to the optical spin (degree of circular polarization). Such an optical force was recently predicted for evanescent waves and other structured fields. It can be associated with the ’spin-momentum’ part of the Poynting vector, introduced by Belinfante in field theory 75 years ago. We measure this unusual transverse momentum using a femtonewton-resolution nano-cantilever immersed in an evanescent optical field above the total internal reflecting glass surface. Furthermore, the measured transverse force exhibits another polarization-dependent contribution determined by the imaginary part of the complex Poynting vector. By revealing new types of optical forces in structured fields, our findings revisit fundamental momentum properties of light and enrich optomechanics.


Bond rupture between colloidal particles with a depletion interaction

Kathryn A. Whitaker and Eric M. Furst

The force required to break the bonds of a depletion gel is measured by dynamically loading pairs of colloidal particles suspended in a solution of a nonadsorbing polymer. Sterically stabilized poly(methyl methacrylate) colloids that are 2.7 μm diameter are brought into contact in a solvent mixture of cyclohexane-cyclohexyl bromide and polystyrene polymer depletant. The particle pairs are subject to a tensile load at a constant loading rate over many approach-retraction cycles. The stochastic nature of the thermal rupture events results in a distribution of bond rupture forces with an average magnitude and variance that increases with increasing depletant concentration. The measured force distribution is described by the flux of particle pairs sampling the energy barrier of the bond interaction potential based on the Asakura–Oosawa depletion model. A transition state model demonstrates the significance of lubricationhydrodynamic interactions and the effect of the applied loading rate on the rupture force of bonds in a depletion gel.

Exposure to TiO2 nanoparticles increases Staphylococcus aureus infection of HeLa cells

Yan Xu, Ming-Tzo Wei, H. Daniel Ou-Yang, Stephen G. Walker, Hong Zhan Wang, Chris R. Gordon, Shoshana Guterman, Emma Zawacki, Eliana Applebaum, Peter R. Brink, Miriam Rafailovich and Tatsiana Mironava

Titanium dioxide (TiO2) is one of the most common nanoparticles found in industry ranging from food additives to energy generation. Approximately four million tons of TiO2 particles are produced worldwide each year with approximately 3000 tons being produced in nanoparticulate form, hence exposure to these particles is almost certain.
Even though TiO2 is also used as an anti-bacterial agent in combination with UV, we have found that, in the absence of UV, exposure of HeLa cells to TiO2 nanoparticles significantly increased their risk of bacterial invasion. HeLa cells cultured with 0.1 mg/ml rutile and anatase TiO2 nanoparticles for 24 h prior to exposure to bacteria had 350 and 250 % respectively more bacteria per cell. The increase was attributed to bacterial polysaccharides absorption on TiO2 NPs, increased extracellular LDH, and changes in the mechanical response of the cell membrane. On the other hand, macrophages exposed to TiO2 particles ingested 40 % fewer bacteria, further increasing the risk of infection.
In combination, these two factors raise serious concerns regarding the impact of exposure to TiO2 nanoparticles on the ability of organisms to resist bacterial infection.


Relevance of interfacial viscoelasticity in stability and conformation of biomolecular organizates at air/fluid interface

M. Steffi Antony, Jaganathan Maheshkumar, Aruna Dhathathreyan

Soft materials are complex macromolecular systems often exhibiting perplexing non-Newtonian viscoelastic properties, especially when the macromolecules are entangled, crowded or cross-linked. These materials are ubiquitous in biology, food and pharma industry and have several applications in biotechnology and in the field of biosensors. Based on the length scales, topologies, flexibility and concentration, the systems behave both as liquids (viscous) and solids (elastic). Particularly, for proteins and protein-lipid systems, viscoelasticity is an important parameter because it often relates directly to stability and thermodynamic interactions of the pure biological components as well as their mixtures. Despite the large body of work that is available in solution macro-rheometry, there remain still a number of issues that need to be addressed in dealing with proteins at air/fluid interfaces and with protein-polymer or protein-lipid interfaces that often exhibit very low interfacial viscosity values.
Considering the important applications that they have in biopharmaceutical, biotechnological and nutraceutical industries, there is a need for developing methods that meet the following three specific issues: small volume; large dynamic range of shear rates; and interfacial properties of different biomolecules. Further, the techniques that are developed should include Newtonian, shear thinning and yielding properties, which are representative of the different solution behaviors typically encountered. The review presented here is a comprehensive account of the rheological properties of different biomolecules at air/fluid and solid/fluid interfaces. It addresses the usefulness of ‘viscoelasticity’ of the systems at the interfaces analyzed at the molecular level that can be correlated with the microscopic material properties and touches upon some recent techniques in microrheology that are being used to measure the unusually low viscosity values sensitively.


Swollen structure and electrostatic interactions of polyelectrolyte brush in aqueous solution

Daiki Murakami, Motoyasu Kobayashi, Yuji Higaki, Hiroshi Jinnai, Atsushi Takahara

Surface grafting of polyelectrolytes on materials brings about various significant changes in surface properties such as wettability, adhesion, and friction, because of their excellent hydrophilicity and unique intermolecular interactions that depend on the ionic strength of the solution. This review paper describes the characterization of the swollen structure and electrostatic interaction of polyelectrolyte brushes in aqueous solution by use of optical tweezers and neutron reflectivity, in order to discuss the dissociation of ionic groups and charge distribution in the polyelectrolyte brush. In addition, the spreading and structure of water on the polyelectrolyte brush surface were characterized by high spatial resolution IR spectroscopy.