The fluctuation-dissipation relation holds for a macroscopic tracer in an active bath.

The fluctuation-dissipation relation (FDR) links thermal fluctuations and dissipation at thermal equilibrium through temperature. Extending it beyond equilibrium conditions in pursuit of broadening thermodynamics is often feasible, albeit with system-dependent specific conditions. We demonstrate experimentally that a generalized FDR holds for a harmonically trapped tracer colliding with self-propelled walkers.

Ebola Virus Glycoprotein Strongly Binds to Membranes in the Absence of Receptor Engagement.

Ebola virus (EBOV) is an enveloped virus that must fuse with the host cell membrane in order to release its genome and initiate infection. This process requires the action of the EBOV envelope glycoprotein (GP), encoded by the virus, which resides in the viral envelope and consists of a receptor binding subunit, GP1, and a membrane fusion subunit, GP2. Despite extensive research, a mechanistic understanding of the viral fusion process is incomplete.

Programmable comprehensive controller for multi-color 3D confocal spinning-disk image scanning microscope.

This paper introduces a compact, portable, and highly accurate triggering control system for a 3D confocal spinning-disk image scanning microscope (CSD-ISM). Building upon on our previously published research, we expanded the hardware of the controller and synchronized it with a sub-micron translator which scans the object in the z-direction. As well as expanding the hardware, the software also was extended from previously published work similarly as it is stated for hardware while allowing full control over the 3D movement.

Portable low-cost and highly accurate programmable triggering controller for confocal spinning disk image scanning microscope.

This work presents a very low-cost and highly accurate alternative way of implementing triggering control for a confocal spinning-disk image scanning microscope (CSD-ISM). Instead of using the previously reported hig-cost field programmable gate array (FPGA), that connects to a computer by an internal PCIe bus, we implemented the controller using a simple, low-cost real-time digital signal controller (DSC) development kit that connects to a computer via an external USB channel. The overall time resolution of the controller is better than 10 nanoseconds.

Diffusion with partial resetting.

Inspired by many examples in nature, stochastic resetting of random processes has been studied extensively in the past decade. In particular, various models of stochastic particle motion were considered where, upon resetting, the particle is returned to its initial position. Here we generalize the model of diffusion with resetting to account for situations where a particle is returned only a fraction of its distance to the origin, e.

Spatial Crossover Between Far-From-Equilibrium and Near-Equilibrium Dynamics in Locally Driven Suspensions.

We examine the response of a quasi-two-dimensional colloidal suspension to a localized circular driving induced by optical tweezers. This approach allows us to resolve over 3 orders of magnitude in the Péclet number (Pe) and provide a direct observation of a sharp spatial crossover from far- to near-thermal-equilibrium regions of the suspension. In particular, particles migrate from high to low Pe regions and form strongly inhomogeneous steady-state density profiles with an emerging length scale that does not depend on the particle density and is set by Pe≈1.

Measurements and characterization of the dynamics of tracer particles in an actin network.

The underlying physics governing the diffusion of a tracer particle in a viscoelastic material is a topic of some dispute. The long-term memory in the mechanical response of such materials should induce diffusive motion with a memory kernel, such as fractional Brownian motion (fBM). This is the reason that microrheology is able to provide the shear modulus of polymer networks.

Correction: Live cell single molecule tracking and localization microscopy of bioorthogonally labeled plasma membrane proteins.

Correction for 'Live cell single molecule tracking and localization microscopy of bioorthogonally labeled plasma membrane proteins' by Andres I. König et al., Nanoscale, 2020, 12, 3236-3248, DOI: 10.

Kinetics of actin networks formation measured by time resolved particle-tracking microrheology.

Actin is one of the most studied cytoskeleton proteins showing a very rich span of structures and functions. For example, adenosine triphosphate (ATP)-assisted polymerization of actin is used to push protrusions forward in a mechanism that enables cells to crawl on a substrate. In this process, the chemical energy released from the hydrolysis of ATP is what enables force generation.

Experimental Realization of Diffusion with Stochastic Resetting.

Stochastic resetting is prevalent in natural and man-made systems, giving rise to a long series of nonequilibrium phenomena. Diffusion with stochastic resetting serves as a paradigmatic model to study these phenomena, but the lack of a well-controlled platform by which this process can be studied experimentally has been a major impediment to research in the field. Here, we report the experimental realization of colloidal particle diffusion and resetting via holographic optical tweezers.

Live cell single molecule tracking and localization microscopy of bioorthogonally labeled plasma membrane proteins.

Tracking the localization and mobility of individual proteins in live cells is key for understanding how they mediate their function. Such information can be obtained from single molecule imaging techniques including as Single Particle Tracking (SPT) and Single Molecule Localization Microscopy (SMLM). Genetic code expansion (GCE) combined with bioorthogonal chemistry offers an elegant approach for direct labeling of proteins with fluorescent dyes, holding great potential for improving protein labeling in single molecule applications.

Auxiliary Optomechanical Tools for 3D Cell Manipulation.

Advances in laser and optoelectronic technologies have brought the general concept of optomechanical manipulation to the level of standard biophysical tools, paving the way towards controlled experiments and measurements of tiny mechanical forces. Recent developments in direct laser writing (DLW) have enabled the realization of new types of micron-scale optomechanical tools, capable of performing designated functions. Here we further develop the concept of DLW-fabricated optomechanically-driven tools and demonstrate full-3D manipulation capabilities over biological objects.

Real-Time In-Situ Monitoring of a Tunable Pentapeptide Gel-Crystal Transition.

Supramolecular gels often become destabilized by the transition of the gelator into a more stable crystalline phase, but often the long timescale and sporadic localization of the crystalline phase preclude a persistent observation of this process. We present a pentapeptide gel-crystal phase transition amenable for continuous visualization and quantification by common microscopic methods, allowing the extraction of kinetics and visualization of the dynamics of the transition. Using optical microscopy and microrheology, we show that the transition is a sporadic event in which gel dissolution is associated with microcrystalline growth that follows a sigmoidal rate profile.

Nanoparticle Mobility over a Surface as a Probe for Weak Transient Disordered Peptide-Peptide Interactions.

Weak interactions form the core basis of a vast number of biological processes, in particular, those involving intrinsically disordered proteins. Here, we establish a new technique capable of probing these weak interactions between synthetic unfolded polypeptides using a convenient yet efficient, quantitative method based on single particle tracking of peptide-coated gold nanoparticles over peptide-coated surfaces. We demonstrate that our technique is sensitive enough to observe the influence of a single amino acid mutation on the transient peptide-peptide interactions.

Flow Arrest in the Plasma Membrane.

The arrangement of receptors in the plasma membrane strongly affects the ability of a cell to sense its environment both in terms of sensitivity and in terms of spatial resolution. The spatial and temporal arrangement of the receptors is affected in turn by the mechanical properties and the structure of the cell membrane. Here, we focus on characterizing the flow of the membrane in response to the motion of a protein embedded in it.

Single-Particle Diffusion Characterization by Deep Learning.

Diffusion plays a crucial role in many biological processes including signaling, cellular organization, transport mechanisms, and more. Direct observation of molecular movement by single-particle-tracking experiments has contributed to a growing body of evidence that many cellular systems do not exhibit classical Brownian motion but rather anomalous diffusion. Despite this evidence, characterization of the physical process underlying anomalous diffusion remains a challenging problem for several reasons.

Optical trapping below the diffraction limit with a tunable beam waist using super-oscillating beams.

Super-oscillating beams can be used to create light spots whose size is below the diffraction limit with a side ring of high intensity adjacent to them. Optical traps made of the super-oscillating part of such beams exhibit superior localization of submicron beads compared to regular optical traps. Here we focus on the effect of the ratio of particle size to beam size on the localization and stiffness of optical traps made of super-oscillating beams.

Deep-penetration fluorescence imaging through dense yeast cells suspensions using Airy beams.

We propose, to the best of our knowledge, a new method to image fluorescent objects through turbid media based on Airy beam scanning. This is achieved by using the nondiffractive nature of Airy beams, namely their ability to maintain their shape while penetrating through a highly scattering medium. We show that our technique can image fluorescent objects immersed in turbid media with higher resolution and signal to noise than confocal imaging.

Structural changes in nanoparticle-hydrogel composites at very low filler concentrations.

We study the enhancement of the stiffness of two families of hydrogels (polyacrylamide, PAAm, and polydimethylacrylamide, PDMA) due to the additions of very small amounts of silica nanofillers. It is well established that high concentrations of silica nanoparticles enhance the toughness of both hydrogel types, but significantly more for the PDMA based gels that adsorb readily to silica surfaces. In order to decouple the structural changes in the gels that stem either from polymerization kinetics or from the interactions between nanofillers and polymers, we use a photoinitiator for the polymerization of the composite gels that promotes the structural homogeneity of the hydrogels.

Experimental Realization of an Information Machine with Tunable Temporal Correlations.

We experimentally realize a Maxwell's demon that converts information gained by measurements to work. Our setup is composed of a colloidal particle in a channel filled with a flowing fluid. A barrier made by light prevents the particle from being carried away by the flow.

Fluorescent Tracking of the Endoplasmic Reticulum in Live Pathogenic Fungal Cells.

In fungal cells, the endoplasmic reticulum (ER) harbors several of the enzymes involved in the biosynthesis of ergosterol, an essential membrane component, making this organelle the site of action of antifungal azole drugs, used as a first-line treatment for fungal infections. This highlights the need for specific fluorescent labeling of this organelle in cells of pathogenic fungi. Here we report on the development and evaluation of a collection of fluorescent ER trackers in a panel of Candida, considered the most frequently encountered pathogen in fungal infections.

Particle manipulation beyond the diffraction limit using structured super-oscillating light beams.

The diffraction-limited resolution of light focused by a lens was derived in 1873 by Ernst Abbe. Later in 1952, a method to reach sub-diffraction light spots was proposed by modulating the wavefront of the focused beam. In a related development, super-oscillating functions, that is, band-limited functions that locally oscillate faster than their highest Fourier component, were introduced and experimentally applied for super-resolution microscopy.

Non-diffracting beams for label-free imaging through turbid media.

We propose a new method to image through dynamically changing turbid media based on the scanning of non-diffractive laser beams. We use computer-generated holograms to create Airy beams and compare quantitatively the characteristics of their propagation in clear and turbid media. Imaging contrast is achieved by relative reflection of the scanned beams from the imaged surface.

Scale dependence of the mechanics of active gels with increasing motor concentration.

Actin is a protein that plays an essential role in maintaining the mechanical integrity of cells. In response to strong external stresses, it can assemble into large bundles, but it grows into a fine branched network to induce cell motion. In some cases, the self-organization of actin fibers and networks involves the action of bipolar filaments of the molecular motor myosin.

Real-Time Imaging of the Azole Class of Antifungal Drugs in Live Candida Cells.

Azoles are the most commonly used class of antifungal drugs, yet where they localize within fungal cells and how they are imported remain poorly understood. Azole antifungals target lanosterol 14α-demethylase, a cytochrome P450, encoded by ERG11 in Candida albicans, the most prevalent fungal pathogen. We report the synthesis of fluorescent probes that permit visualization of antifungal azoles within live cells.