Broad Adaptability of Coronavirus Adhesion Revealed from the Complementary Surface Affinity of Membrane and Spikes.

Coronavirus stands for a large family of viruses characterized by protruding spikes surrounding a lipidic membrane adorned with proteins. The present study explores the adhesion of transmissible gastroenteritis coronavirus (TGEV) particles on a variety of reference solid surfaces that emulate typical virus-surface interactions. Atomic force microscopy informs about trapping effectivity and the shape of the virus envelope on each surface, revealing that the deformation of TGEV particles spans from 20% to 50% in diameter. Given this large deformation range, experimental Langmuir isotherms convey an unexpectedly moderate variation in the adsorption-free energy, indicating a viral adhesion adaptability which goes beyond the membrane. The combination of an extended Helfrich theory and coarse-grained simulations reveals that, in fact, the envelope and the spikes present complementary adsorption affinities. While strong membrane-surface interaction lead to highly deformed TGEV particles, surfaces with strong spike attraction yield smaller deformations with similar or even larger adsorption-free energies.

Multiparametric modulation of magnetic transduction for biomolecular sensing in liquids.

The recent COVID19 pandemic has remarkably boosted the research on in vitro diagnosis assays to detect biomarkers in biological fluids. Specificity and sensitivity are mandatory for diagnostic kits aiming to reach clinical stages. Whilst the modulation of sensitivity can significantly improve the detection of biomarkers in liquids, this has been scarcely explored. Here, we report on the proof of concept and parametrization of a novel biosensing methodology based on the changes of AC magnetic hysteresis areas observed for magnetic nanoparticles following biomolecular recognition in liquids. Several parameters are shown to significantly modulate the transducing capacity of magnetic nanoparticles to detect analytes dispersed in saline buffer at concentrations of clinical relevance. Magnetic nanoparticles were bio-conjugated with an engineered recognition peptide as a receptor. Analytes are engineered tetratricopeptide binding domains fused to the fluorescent protein whose dimerization state allows mono- or divalent variants. Our results unveil that the number of receptors per particle, analyte valency and concentration, nanoparticle composition and concentration, and field conditions play a key role in the formation of assemblies driven by biomolecular recognition. Consequently, all these parameters modulate the nanoparticle transduction capacity. Our study provides essential insights into the potential of AC magnetometry for customizing biomarker detection in liquids.

Coverage Effects in Quartz Crystal Microbalance Measurements with Suspended and Adsorbed Nanoparticles.

Quartz crystal microbalance (QCM) biosensors often deal with nanoparticles suspended in the solvent at tens of nanometers above the resonator while being linked to some molecular receptor (DNA, antibody, etc.). This work presents a numerical analysis based on the immersed boundary method for the flow and QCM impedance created by an ensemble of spherical particles of radius R at varying surface coverage Θ and particle-surface gap distance Δ. The trends for the frequency Δf and dissipation ΔD shifts against Θ and Δ are shown to be determined by modifications in the structure of the perturbative flow created by the analytes. Simulations are in good agreement with a relatively large experimental database collected from the literature. Qualitative differences between the adsorbed (Δ ≈ 0) and suspended states (Δ > 0) are highlighted. In the case of adsorbed particles, deviations from the linear scaling Δf ∝ Θ are observed above Θ > 0.05 and largely depend on the specific analyte-substrate combination. Moreover, in general, ΔD(Θ) is not monotonous and usually presents a maximum around Θ âˆ¼ 0.2. In the case of suspended analytes, the agreement with the numerical results is quantitative, indicating that the predicted scalings are universal and determined by hydrodynamics. Up to high coverage, the suspended particles present Δf ∼ Θ and ΔD ∼ Θß, where ß ≈ 0.85 is not largely dependent on R. The present findings should help forecast molecular configurations from QCM signals and have implications on QCM analyses, e.g., in the case of suspended ligands (Δf ∝ Θ), it is safe to use Δf to build Langmuir isotherms and estimate equilibrium constants. Open questions on the transition from the suspended-to-adsorbed state are discussed.

Boosting the efficiency of transient photoluminescence microscopy using cylindrical lenses.

Transient Photoluminescence Microscopy (TPLM) allows for the direct visualization of carrier transport in semiconductor materials with sub nanosecond and few nanometer resolution. The technique is based on measuring changes in the spatial distribution of a diffraction limited population of carriers using spatiotemporal detection of the radiative decay of the carriers. The spatial resolution of TPLM is therefore primarily determined by the signal-to-noise-ratio (SNR). Here we present a method using cylindrical lenses to boost the signal acquisition in TPLM experiments. The resulting asymmetric magnification of the photoluminescence emission of the diffraction limited spot can increase the collection efficiency by more than a factor of 10, significantly reducing acquisition times and further boosting spatial resolution.

Predicting the size and morphology of nanoparticle clusters driven by biomolecular recognition.

Nanoparticle aggregation is a driving principle of innovative materials and biosensing methodologies, improving transduction capabilities displayed by optical, electrical or magnetic measurements. This aggregation can be driven by the biomolecular recognition between target biomolecules (analytes) and receptors bound onto nanoparticle surface. Despite theoretical advances on modelling the entropic interaction in similar systems, predictions of the fractal morphologies of the nanoclusters of bioconjugated nanoparticles are lacking. The morphology of resulting nanoclusters is sensitive to the location, size, flexibility, average number of receptors per particle f̄, and the analyte-particle concentration ratio. Here we considered bioconjugated iron oxide nanoparticles (IONPs) where bonds are mediated by a divalent protein that binds two receptors attached onto different IONPs. We developed a protocol combining analytical expressions for receptors and linker distributions, and Brownian dynamics simulations for bond formation, and validated it against experiments. As more bonds become available (e.g., by adding analytes), the aggregation deviates from the ideal Bethe's lattice scenario due to multivalence, loop formation, and steric hindrance. Generalizing Bethe's lattice theory with a (not-integer) effective functionality feff leads to analytical expressions for the cluster size distributions in excellent agreement with simulations. At high analyte concentration steric impediment imposes an accessible limit value facc to feff, which is bounded by facc < feff < f̄. A transition to gel phase, is correctly captured by the derived theory. Our findings offer new insights into quantifying analyte amounts by assessing nanocluster size, and predicting nanoassembly morphologies accurately is a first step towards understanding variations of physical properties in clusters formed after biomolecular recognition.

Unravelling 3D Dynamics and Hydrodynamics during Incorporation of Dielectric Particles to an Optical Trapping Site.

Mapping of the spatial and temporal motion of particles inside an optical field is critical for understanding and further improvement of the 3D spatio-temporal control over their optical trapping dynamics. However, it is not trivial to capture the 3D motion, and most imaging systems only capture a 2D projection of the 3D motion, in which the information about the axial movement is not directly available. In this work, we resolve the 3D incorporation trajectories of 200 nm fluorescent polystyrene particles in an optical trapping site under different optical experimental conditions using a recently developed widefield multiplane microscope (imaging volume of 50 × 50 × 4 µm3). The particles are gathered at the focus following some preferential 3D channels that show a shallow cone distribution. We demonstrate that the radial and the axial flow speed components depend on the axial distance from the focus, which is directly related to the scattering/gradient optical forces. While particle velocities and trajectories are mainly determined by the trapping laser profile, they cannot be completely explained without considering collective effects resulting from hydrodynamic forces.

Electromechanical Photophysics of GFP Packed Inside Viral Protein Cages Probed by Force-Fluorescence Hybrid Single-Molecule Microscopy.

Packing biomolecules inside virus capsids has opened new avenues for the study of molecular function in confined environments. These systems not only mimic the highly crowded conditions in nature, but also allow their manipulation at the nanoscale for technological applications. Here, green fluorescent proteins are packed in virus-like particles derived from P22 bacteriophage procapsids. The authors explore individual virus cages to monitor their emission signal with total internal reflection fluorescence microscopy while simultaneously changing the microenvironment with the stylus of atomic force microscopy. The mechanical and electronic quenching can be decoupled by ≈10% each using insulator and conductive tips, respectively. While with conductive tips the fluorescence quenches and recovers regardless of the structural integrity of the capsid, with the insulator tips quenching only occurs if the green fluorescent proteins remain organized inside the capsid. The electronic quenching is associated with the coupling of the protein fluorescence emission with the tip surface plasmon resonance. In turn, the mechanical quenching is a consequence of the unfolding of the aggregated proteins during the mechanical disruption of the capsid.

Hydrodynamics induce superdiffusive jumps of passive tracers along critical paths of random networks and colloidal gels.

We present a numerical study on the effect of hydrodynamic interactions (HI) on the diffusion of inert point tracer particles in several fixed random structures. As expected, the diffusion is hampered by the extra hydrodynamic friction introduced by the obstacle network. However, a non-trivial effect due to HI appears in the analysis of the van-Hove displacement probability close to the percolation threshold, where tracers diffuse through critical fractal paths. We show that the tracer dynamics can be split up into short and long jumps, the latter being ruled by either exponential or Gaussian van Hove distribution tails. While at short time HI slow down the tracer diffusion, at long times, hydrodynamic interactions with the obstacles increase the probability of longer jumps, which circumvent the traps of the labyrinth more easily. Notably, the relation between the anomalous diffusion exponent and the fractal dimension of the critical (intricate) paths is greater than one, which implies that the long-time (long-jump) diffusion is mildly superdiffuse. A possible reason for such a hastening of the diffusion along the network corridors is the hydrodynamically induced mobility anisotropy, which favours displacements parallel to the walls, an effect which has already been experimentally observed in collagen gels.

Halide Mixing Inhibits Exciton Transport in Two-dimensional Perovskites Despite Phase Purity.

Halide mixing is one of the most powerful techniques to tune the optical bandgap of metal-halide perovskites. However, halide mixing has commonly been observed to result in phase segregation, which reduces excited-state transport and limits device performance. While the current emphasis lies on the development of strategies to prevent phase segregation, it remains unclear how halide mixing may affect excited-state transport even if phase purity is maintained. Here, we study exciton transport in phase pure mixed-halide 2D perovskites of (PEA)2Pb(I1-x Br x )4. Using transient photoluminescence microscopy, we show that, despite phase purity, halide mixing inhibits exciton transport. We find a significant reduction even for relatively low alloying concentrations. By performing Brownian dynamics simulations, we are able to reproduce our experimental results and attribute the decrease in diffusivity to the energetically disordered potential landscape that arises due to the intrinsic random distribution of alloying sites.

Quantitative description of the response of finite size adsorbates on a quartz crystal microbalance in liquids using analytical hydrodynamics.

Despite being a fundamental tool in soft matter research and biosensing, quartz crystal microbalance (QCM) analyses of discrete macromolecules in liquids so far lack a firm theoretical basis. Quite often, acoustic signals of discrete particles are qualitatively interpreted using ad hoc frameworks based on effective electrical circuits, effective springs and trapped-solvent models with many fitting parameters. Nevertheless, due to its extreme sensitivity, the QCM technique pledges to become an accurate predictive tool. Using unsteady low Reynolds hydrodynamics we derive analytical expressions for the acoustic impedance of adsorbed discrete spheres. The present approach is successfully validated against 3D simulations and a plethora of experimental results covering more than a decade of research on proteins, viruses, liposomes, and massive nanoparticles, with sizes ranging from a few to hundreds of nanometers. The agreement without fitting parameters indicates that the acoustic response is dominated by the hydrodynamic propagation of the particle surface stress over the resonator. Understanding this leading contribution is a prerequisite for deciphering the secondary contributions arising from the relevant specific molecular and physico-chemical forces.

Load Impedance of Immersed Layers on the Quartz Crystal Microbalance: A Comparison with Colloidal Suspensions of Spheres.

The analytical theories derived here for the acoustic load impedance measured by a quartz crystal microbalance (QCM), due to the presence of layers of different types (rigid, elastic, and viscous) immersed in a fluid, display generic properties, such as "vanishing mass" and positive frequency shifts, which have been observed in QCM experiments with soft-matter systems. These phenomena seem to contradict the well-known Sauerbrey relation at the heart of many QCM measurements, but here, we show that they arise as a natural consequence of hydrodynamics. We compare our one-dimensional immersed plate theory with three-dimensional simulations of rigid and flexible submicron-sized suspended spheres and with experimental results for adsorbed micron-sized colloids, which yield a "negative acoustic mass". The parallel behavior unveiled indicates that the QCM response is highly sensitive to hydrodynamics, even for adsorbed colloids. Our conclusions call for a revision of existing theories based on adhesion forces and elastic stiffness at contact, which should, in most cases, include hydrodynamics.

Exciton diffusion in two-dimensional metal-halide perovskites.

Two-dimensional layered perovskites are attracting increasing attention as more robust analogues to the conventional three-dimensional metal-halide perovskites for both light harvesting and light emitting applications. However, the impact of the reduced dimensionality on the optoelectronic properties remains unclear, particularly regarding the spatial dynamics of the excitonic excited state within the two-dimensional plane. Here, we present direct measurements of exciton transport in single-crystalline layered perovskites. Using transient photoluminescence microscopy, we show that excitons undergo an initial fast diffusion through the crystalline plane, followed by a slower subdiffusive regime as excitons get trapped. Interestingly, the early intrinsic diffusivity depends sensitively on the choice of organic spacer. A clear correlation between lattice stiffness and diffusivity is found, suggesting exciton-phonon interactions to be dominant in the spatial dynamics of the excitons in perovskites, consistent with the formation of exciton-polarons. Our findings provide a clear design strategy to optimize exciton transport in these systems.

Boundary conditions derived from a microscopic theory of hydrodynamics near solids.

The theory of nonlocal isothermal hydrodynamics near a solid object derived microscopically in the study by Camargo et al. [J. Chem. Phys. 148, 064107 (2018)] is considered under the conditions that the flow fields are of macroscopic character. We show that in the limit of macroscopic flows, a simple pillbox argument implies that the reversible and irreversible forces that the solid exerts on the fluid can be represented in terms of boundary conditions. In this way, boundary conditions are derived from the underlying microscopic dynamics of the fluid-solid system. These boundary conditions are the impenetrability condition and the Navier slip boundary condition. The Green-Kubo transport coefficients associated with the irreversible forces that the solid exert on the fluid appear naturally in the slip length. The microscopic expression for the slip length thus obtained is shown to coincide with the one provided originally by Bocquet and Barrat [Phys. Rev. E 49, 3079 (1994)].

Upconverting Nanorockers for Intracellular Viscosity Measurements During Chemotherapy.

Chemicals capable of producing structural and chemical changes on cells are used to treat diseases (e.g., cancer). Further development and optimization of chemotherapies require thorough knowledge of the effect of the chemical on the cellular structure and dynamics. This involves studying, in a noninvasive way, the properties of individual cells after drug administration. Intracellular viscosity is affected by chemical treatments and it can be reliably used to monitor chemotherapies at the cellular level. Here, cancer cell monitoring during chemotherapeutic treatments is demonstrated using intracellular allocated upconverting nanorockers. A simple analysis of the polarized visible emission of a single particle provides a real-time readout of its rocking dynamics that are directly correlated to the cytoplasmic viscosity. Numerical simulations and immunodetection are used to correlate the measured intracellular viscosity alterations to the changes produced in the cytoskeleton of cancer cells by anticancer drugs (colchicine and Taxol). This study evidences the possibility of monitoring cellular properties under an external chemical stimulus for the study and development of new treatments. Moreover, it provides the biomedical community with new tools to study intracellular dynamics and cell functioning.

A general phenomenological relation for the subdiffusive exponent of anomalous diffusion in disordered media.

This work numerically investigates the diffusion of finite inert tracer particles in different types of fixed gels. The mean square displacement (MSD) of the tracers reveals a transition to subdiffusive motion MSD ∼ tα as soon as the accessible volume fraction p in the gel decreases from unity. Individual tracer dynamics reveals two types of particles in the gels: mobile tracers cross the system through percolating pores following subdiffusive dynamics MSDmob ∼ tαmob, while a fraction ptrap(p) of the particles remain trapped in finite pores. Below the void percolation threshold p < pc all the particles get trapped and α → 0. By separately studying both populations we find a simple phenomenological law for the mobile tracers αmob(p) ≈ a ln p + c where c ≈ 1 and a ∼ 0.2 depends on the gel type. On the other hand, a cluster-analysis of the gel accessible volume reveals a power law for the trapping probability ptrap ∼ (p/pc)-γ, with γ ≃ 2.9. This yields a prediction for the ensemble averaged subdiffusion exponent α = αmob(1 - ptrap). Our predictions are successfully validated against the different gels studied here and against numerical and experimental results in the literature (silica gels, polyacrylamide gels, flexible F-actin networks and in different random obstacles). Notably, the parameter a ∼ 0.2 presents small differences amongst all these cases, indicating the robustness of the proposed relation.

Nanoscale hydrodynamics near solids.

Density Functional Theory (DFT) is a successful and well-established theory for the study of the structure of simple and complex fluids at equilibrium. The theory has been generalized to dynamical situations when the underlying dynamics is diffusive as in, for example, colloidal systems. However, there is no such a clear foundation for Dynamic DFT (DDFT) for the case of simple fluids in contact with solid walls. In this work, we derive DDFT for simple fluids by including not only the mass density field but also the momentum density field of the fluid. The standard projection operator method based on the Kawasaki-Gunton operator is used for deriving the equations for the average value of these fields. The solid is described as featureless under the assumption that all the internal degrees of freedom of the solid relax much faster than those of the fluid (solid elasticity is irrelevant). The fluid moves according to a set of non-local hydrodynamic equations that include explicitly the forces due to the solid. These forces are of two types, reversible forces emerging from the free energy density functional, and accounting for impenetrability of the solid, and irreversible forces that involve the velocity of both the fluid and the solid. These forces are localized in the vicinity of the solid surface. The resulting hydrodynamic equations should allow one to study dynamical regimes of simple fluids in contact with solid objects in isothermal situations.

The entropy of a complex molecule.

Entropy is a central concept in the theory of coarse-graining. Through Einstein's formula, it provides the equilibrium probability distribution of the coarse-grained variables used to describe the system of interest. We study with molecular dynamics simulations the equilibrium probability distribution of thermal blobs representing at a coarse-grained level star polymer molecules in melt. Thermal blobs are characterized by the positions and momenta of the centers of mass, and internal energies of the molecules. We show that the entropy of the level of description of thermal blobs can be very well approximated as the sum of the thermodynamic entropy of each single molecule considered as isolated thermodynamic systems. The entropy of a single molecule depends on the intrinsic energy, involving only contributions from the atoms that make the molecule and not from the interactions with atoms of other molecules.

Application of the Eckart frame to soft matter: rotation of star polymers under shear flow.

The Eckart co-rotating frame is used to analyze the dynamics of star polymers under shear flow, either in melt or solution and with different types of bonds. This formalism is compared with the standard approach used in many previous studies on polymer dynamics, where an apparent angular velocity ω is obtained from the relation between the tensor of inertia and angular momentum. A common mistake is to interpret ω as the molecular rotation frequency, which is only valid for rigid-body rotation. The Eckart frame, originally formulated to analyze the infrared spectra of small molecules, dissects different kinds of displacements: vibrations without angular momentum, pure rotation, and vibrational angular momentum (leading to a Coriolis cross-term). The Eckart frame co-rotates with the molecule with an angular frequency Ω obtained from the Eckart condition for minimal coupling between rotation and vibration. The standard and Eckart approaches are compared with a straight description of the star's dynamics taken from the time autocorrelation of the monomer positions moving around the molecule's center of mass. This is an underdamped oscillatory signal, which can be described by a rotation frequency ωR and a decorrelation rate Γ. We consistently find that Ω coincides with ωR, which determines the characteristic tank-treading rotation of the star. By contrast, the apparent angular velocity ω < Ω does not discern between pure rotation and molecular vibrations. We believe that the Eckart frame will be useful to unveil the dynamics of semiflexible molecules where rotation and deformations are entangled, including tumbling, tank-treading motions and breathing modes.

Deciphering the dynamics of star molecules in shear flow.

This work analyses the rotation of star polymers under shear flow, in melts, and in good solvent dilute solution. The latter is modeled by single molecule Brownian hydrodynamics, while melts are modeled using non-equilibrium molecular dynamics in closed (periodic) boxes and in open boundaries. A Dissipative Particle Dynamics (DPD) thermostat introduces pairwise monomer friction in melts at will, in directions normal and tangent to the monomer-monomer vectors. Although tangential friction is seldom modeled, we show that it is essential to control hydrodynamic effects in melts. We analyze the different sources of molecular angular momentum in solution and melts and distinguish three dynamic regimes as the shear rate [small gamma, Greek, dot above] is increased. These dynamic regimes are related with the disruption of the different relaxation mechanisms of the star in equilibrium. Although strong differences are found between harmonic springs and finitely extensible bonds, above a critical shear rate the star molecule has a "breathing" mode with successive elongations and contractions in the flow direction with frequency Ω. The force balance in the flow direction unveils a relation between Ω and the orientation angle. Using literature results for the tumbling of rings and linear chains, either in melt or in solution, we show that the relation is general. A different "tank-treading" dynamics determines the rotation of monomers around the center of mass of the molecule. We show that the tank-treading frequency does not saturate but keeps increasing with [small gamma, Greek, dot above]. This is at odds with previous studies which erroneously calculated the molecular angular frequency, used as a proxy for tank-treading.