Monday, December 11, 2017

Image-based model of the spectrin cytoskeleton for red blood cell simulation

Thomas G. Fai , Alejandra Leo-Macias, David L. Stokes, Charles S. Peskin

We simulate deformable red blood cells in the microcirculation using the immersed boundary method with a cytoskeletal model that incorporates structural details revealed by tomographic images. The elasticity of red blood cells is known to be supplied by both their lipid bilayer membranes, which resist bending and local changes in area, and their cytoskeletons, which resist in-plane shear. The cytoskeleton consists of spectrin tetramers that are tethered to the lipid bilayer by ankyrin and by actin-based junctional complexes. We model the cytoskeleton as a random geometric graph, with nodes corresponding to junctional complexes and with edges corresponding to spectrin tetramers such that the edge lengths are given by the end-to-end distances between nodes. The statistical properties of this graph are based on distributions gathered from three-dimensional tomographic images of the cytoskeleton by a segmentation algorithm. We show that the elastic response of our model cytoskeleton, in which the spectrin polymers are treated as entropic springs, is in good agreement with the experimentally measured shear modulus. By simulating red blood cells in flow with the immersed boundary method, we compare this discrete cytoskeletal model to an existing continuum model and predict the extent to which dynamic spectrin network connectivity can protect against failure in the case of a red cell subjected to an applied strain. The methods presented here could form the basis of disease- and patient-specific computational studies of hereditary diseases affecting the red cell cytoskeleton.


Real-time observation of polymerase-promoter contact remodeling during transcription initiation

Cong A. Meng, Furqan M. Fazal & Steven M. Block

Critical contacts made between the RNA polymerase (RNAP) holoenzyme and promoter DNA modulate not only the strength of promoter binding, but also the frequency and timing of promoter escape during transcription. Here, we describe a single-molecule optical-trapping assay to study transcription initiation in real time, and use it to map contacts formed between σ70 RNAP holoenzyme from E. coli and the T7A1 promoter, as well as to observe the remodeling of those contacts during the transition to the elongation phase. The strong binding contacts identified in certain well-known promoter regions, such as the −35 and −10 elements, do not necessarily coincide with the most highly conserved portions of these sequences. Strong contacts formed within the spacer region (−10 to −35) and with the −10 element are essential for initiation and promoter escape, respectively, and the holoenzyme releases contacts with promoter elements in a non-sequential fashion during escape.


Multiplexing molecular tension sensors reveals piconewton force gradient across talin-1

Pia Ringer, Andreas Weißl, Anna-Lena Cost, Andrea Freikamp, Benedikt Sabass, Alexander Mehlich, Marc Tramier, Matthias Rief & Carsten Grashoff

Förster resonance energy transfer (FRET)-based tension sensor modules (TSMs) are available for investigating how distinct proteins bear mechanical forces in cells. Yet, forces in the single piconewton (pN) regime remain difficult to resolve, and tools for multiplexed tension sensing are lacking. Here, we report the generation and calibration of a genetically encoded, FRET-based biosensor called FL-TSM, which is characterized by a near-digital force response and increased sensitivity at 3–5 pN. In addition, we present a method allowing the simultaneous evaluation of coexpressed tension sensor constructs using two-color fluorescence lifetime microscopy. Finally, we introduce a procedure to calculate the fraction of mechanically engaged molecules within cells. Application of these techniques to new talin biosensors reveals an intramolecular tension gradient across talin-1 that is established upon integrin-mediated cell adhesion. The tension gradient is actomyosin- and vinculin-dependent and sensitive to the rigidity of the extracellular environment.


Dual-mode optical fiber-based tweezers for robust trapping and manipulation of absorbing particles in air

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

We develop an optical tweezers system using a single dual-mode optical fiber where mesoscopic absorbing particles can be trapped in three dimensions and manipulated employing photophoretic forces. We generate a superposition of fundamental and first order Hermite–Gaussian beam modes by the simple innovation of coupling a laser into a commercial optical fiber designed to be single mode for a wavelength higher than that of the laser. We achieve robust trapping of the absorbing particles for hours using both the pure fundamental and superposition mode beams and attain large manipulation velocities of ~5 mm s−1 in the axial direction and ~0.75 mm s−1 in the radial direction. We then demonstrate that the superposition mode is more effective in trapping and manipulation compared to the fundamental mode by around 80%, which may be increased several times by the use of a pure first order Hermite–Gaussian mode. The work has promising implications for trapping and spectroscopy of aerosols in air using simple optical fiber-based traps.


Direct measurement of Kramers turnover with a levitated nanoparticle

Loïc Rondin, Jan Gieseler, Francesco Ricci, Romain Quidant, Christoph Dellago & Lukas Novotny

Understanding the thermally activated escape from a metastable state is at the heart of important phenomena such as the folding dynamics of proteins1,2, the kinetics of chemical reactions3 or the stability of mechanical systems4. In 1940, Kramers calculated escape rates both in the high damping and low damping regimes, and suggested that the rate must have a maximum for intermediate damping5. This phenomenon, today known as the Kramers turnover, has triggered important theoretical and numerical studies6. However, as yet, there is no direct and quantitative experimental verification of this turnover. Using a nanoparticle trapped in a bistable optical potential, we experimentally measure the nanoparticle's transition rates for variable damping and directly resolve the Kramers turnover. Our measurements are in agreement with an analytical model that is free of adjustable parameters. The levitated nanoparticle presented here is a versatile experimental platform for studying and simulating a wide range of stochastic processes and testing theoretical models and predictions.


Simultaneous fluorescence and surface charge measurements on organic semiconductor-coated silica microspheres in (non)polar liquids

R. Grollman, G. Founds, R. Wallace, and O. Ostroverkhova

We present an experimental platform which combines spectroscopic capabilities with time-resolved measurements of effective surface charge at solid-liquid interfaces. Silica microspheres, pristine and coated with various organic semiconductor molecules, were optically trapped either in water or in toluene. Adsorption of organic semiconductor molecules on the microspheres was observed via appearance of fluorescence and dramatic reduction in the effective surface charge, measured concurrently on individual spheres, with elementary charge resolution. The versatile platform accommodates possibilities to study a variety of photoinduced processes simultaneously with measurements of surface charge and can be incorporated in devices such as microreactors and microfluidics.


Friday, December 8, 2017

Fast label-free microscopy technique for 3D dynamic quantitative imaging of living cells

José A. Rodrigo, Juan M. Soto, and Tatiana Alieva

The refractive index (RI) is an important optical characteristic that is often exploited in label-free microscopy for analysis of biological objects. A technique for 3D RI reconstruction of living cells has to be fast enough to capture the cell dynamics and preferably needs to be compatible with standard wide-field microscopes. To solve this challenging problem, we present a technique that provides fast measurement and processing of data required for real-time 3D visualization of the object RI. Specifically, the 3D RI is reconstructed from the measurement of bright-field intensity images, axially scanned by a high-speed focus tunable lens mounted in front of a sCMOS camera, by using a direct deconvolution approach designed for partially coherent light microscopy in the non-paraxial regime. Both the measurement system and the partially coherent illumination, that provides optical sectioning and speckle-noise suppression, enable compatibility with wide-field microscopes resulting in a competitive and affordable alternative to the current holographic laser microscopes. Our experimental demonstrations show video-rate 3D RI visualization of living bacteria both freely swimming and optically manipulated by using freestyle laser traps allowing for their trapping and transport along 3D trajectories. These results prove that is possible to conduct simultaneous 4D label-free quantitative imaging and optical manipulation of living cells, which is promising for the study of the cell biophysics and biology.


Universal glass-forming behavior of in vitro and living cytoplasm

Kenji Nishizawa, Kei Fujiwara, Masahiro Ikenaga, Nobushige Nakajo, Miho Yanagisawa & Daisuke Mizuno

Physiological processes in cells are performed efficiently without getting jammed although cytoplasm is highly crowded with various macromolecules. Elucidating the physical machinery is challenging because the interior of a cell is so complex and driven far from equilibrium by metabolic activities. Here, we studied the mechanics of in vitro and living cytoplasm using the particle-tracking and manipulation technique. The molecular crowding effect on cytoplasmic mechanics was selectively studied by preparing simple in vitro models of cytoplasm from which both the metabolism and cytoskeletons were removed. We obtained direct evidence of the cytoplasmic glass transition; a dramatic increase in viscosity upon crowding quantitatively conformed to the super-Arrhenius formula, which is typical for fragile colloidal suspensions close to jamming. Furthermore, the glass-forming behaviors were found to be universally conserved in all the cytoplasm samples that originated from different species and developmental stages; they showed the same tendency for diverging at the macromolecule concentrations relevant for living cells. Notably, such fragile behavior disappeared in metabolically active living cells whose viscosity showed a genuine Arrhenius increase as in typical strong glass formers. Being actively driven by metabolism, the living cytoplasm forms glass that is fundamentally different from that of its non-living counterpart.


Numerical Investigation of Tunable Plasmonic Tweezers based on Graphene Stripes

Mohsen Samadi, Sara Darbari & Mohammad Kazem Moravvej-Farshi

We are proposing tunable plasmonic tweezers, consisting two parallel graphene stripes, which can be utilized to effectively trap and sort nanoparticles. We show that by electrostatically tuning the chemical potential of a graphene stripe by about 100 meV (equivalent to ΔVG ≈ 4.4 V), the plasmonic force can be switched efficiently, without a need to switch the laser intensity. This enables high speed and low power switching with a large number of switching cycles. By applying two independent and appropriate gate bias voltages to the stripes, the direction of the plasmonic force can be reversed, which leads to separation of nanoparticles that satisfy the trapping conditions. Numerical simulations show that the potential depths obtained for polystyrene nanoparticles of refractive index n = 1.5717 and radii r ≥ 50 nm is deeper than −10 kBT , confirming the ability of the proposed system to effectively separate such nanoparticles. This capability holds for smaller nanoparticles with larger refractive indices. Finally, performing thermal simulations, we have demonstrated that the heat induced by the illumination increases the fluid temperature by at most 9 °C, having negligible effect on the trapping mechanism. The proposed system opens up new possibilities in developing tunable on-chip manipulation devices, suitable for biological applications.


Pushing, pulling and electromagnetic radiation force cloaking by a pair of conducting cylindrical particles

F.G. Mitri

The present analysis shows that two conducting cylindrical particles illuminated by an axially-polarized electric field of plane progressive waves at arbitrary incidence will attract, repel or become totally cloaked (i.e., invisible to the transfer of linear momentum carried by the incident waves), depending on their sizes, the interparticle distance as well as the angle of incidence of the incident field. Based on the rigorous multipole expansion method and the translational addition theorem of cylindrical wave functions, the electromagnetic (EM) radiation forces arising from multiple scattering effects between a pair of perfectly conducting cylindrical particles of circular cross-sections are derived and computed. An effective incident field on a particular particle is determined first, and used subsequently with its corresponding scattered field to derive the closed-form analytical expressions for the radiation force vector components. The mathematical expressions for the EM radiation force components (i.e. longitudinal and transverse) are exact, and have been formulated in partial-wave series expansions in cylindrical coordinates involving the angle of incidence, the interparticle distance and the expansion coefficients. Numerical examples illustrate the analysis for two perfectly conducting circular cylinders in a homogeneous nonmagnetic medium of wave propagation. The computations for the dimensionless radiation force functions are performed with particular emphasis on varying the angle of incidence, the interparticle distance, and the sizes of the particles. Depending on the interparticle distance and angle of incidence, the cylinders yield total neutrality (or invisibility); they experience no force and become unresponsive to the transfer of the EM linear momentum due to multiple scattering cancellation effects. Moreover, pushing or pulling EM forces between the two cylinders arise depending on the interparticle distance, the angle of incidence and their size parameters. This study provides a complete analytical method and computations for the longitudinal and transverse radiation force components in the multiple scattering of EM plane progressive waves with potential applications in particle manipulation, optically-engineered metamaterials with reconfigurable periodicities and cloaking devices to name a few examples.