Diffusive dynamics of charged nanoparticles in convex lens-induced confinement

Hydrodynamic effects influence the dynamics of nanoparticles in confined geometries.

Single molecule tracking of bacterial cell surface cytochromes reveals dynamics that impact long-distance electron transport

Using a series of multiheme cytochromes, the metal-reducing bacterium Shewanella oneidensis MR-1 can perform extracellular electron transfer (EET) to respire redox-active surfaces, including minerals and electrodes outside the cell. While the role of multiheme cytochromes in transporting electrons across the cell wall is well established, these cytochromes were also recently found to facilitate long-distance (micrometer-scale) redox conduction along outer membranes and across multiple cells bridging electrodes. Recent studies proposed that long-distance conduction arises from the interplay of electron hopping and cytochrome diffusion, which allows collisions and electron exchange between cytochromes along membranes. However, the diffusive dynamics of the multiheme cytochromes have never been observed or quantified in vivo, making it difficult to assess their hypothesized contribution to the collision-exchange mechanism. Here we use quantum dot labeling, total internal reflection fluorescence microscopy, and single-particle tracking to quantify the lateral diffusive dynamics of the outer membrane-associated decaheme cytochromes MtrC and OmcA, two key components of EET in S. oneidensis. We observe confined diffusion behavior for both quantum dot-labeled MtrC and OmcA along cell surfaces (diffusion coefficients DMtrC = 0.0192 ± 0.0018 μm2/s, DOmcA = 0.0125 ± 0.0024 μm2/s) and the membrane extensions thought to function as bacterial nanowires. We find that these dynamics can trace a path for electron transport via overlap of cytochrome trajectories, consistent with the long-distance conduction mechanism. The measured dynamics inform kinetic Monte Carlo simulations that combine direct electron hopping and redox molecule diffusion, revealing significant electron transport rates along cells and membrane nanowires.

Quantitative theory for the diffusive dynamics of liquid condensates

Key processes of biological condensates are diffusion and material exchange with their environment. Experimentally, diffusive dynamics are typically probed via fluorescent labels. However, to date, a physics-based, quantitative framework for the dynamics of labeled condensate components is lacking. Here we derive the corresponding dynamic equations, building on the physics of phase separation, and quantitatively validate the related framework via experiments. We show that by using our framework we can precisely determine diffusion coefficients inside liquid condensates via a spatio-temporal analysis of fluorescence recovery after photobleaching (FRAP) experiments. We showcase the accuracy and precision of our approach by considering space- and time-resolved data of protein condensates and two different polyelectrolyte-coacervate systems. Interestingly, our theory can also be used to determine a relationship between the diffusion coefficient in the dilute phase and the partition coefficient, without relying on fluorescence measurements in the dilute phase. This enables us to investigate the effect of salt addition on partitioning and bypasses recently described quenching artifacts in the dense phase. Our approach opens new avenues for theoretically describing molecule dynamics in condensates, measuring concentrations based on the dynamics of fluorescence intensities, and quantifying rates of biochemical reactions in liquid condensates.

Dipolariton propagation in a van der Waals TMDC with Ψ-shaped channel guides and buffered channel branches

Using a computational approach based on the driven diffusion equation for dipolariton wave packets, we simulate the diffusive dynamics of dipolaritons in an optical microcavity embedded with a transition metal dichalcogenide (TMDC) heterogeneous bilayer encompassing a [Formula: see text]-shaped channel. By considering exciton-dipolaritons, which are a three-way superposition of direct excitons, indirect excitons and cavity photons, we are able to drive the dipolaritons in our system by the use of an electric voltage and investigate their diffusive properties. More precisely, we study the propagation of dipolaritons present in a MoSe2-WS2 heterostructure, where the dipolariton propagation is guided by a [Formula: see text]-shaped channel. We also consider the propagation of dipolaritons in the presence of a buffer in the [Formula: see text]-shaped channel and study resulting changes in efficiency. We introduce designs for optical routers at room-temperature as well as show that system parameters including driving forces of [Formula: see text] eV/mm and electric field angles of [Formula: see text] optimize the dipolariton redistribution efficiencies in our channel guide.

Hierarchical microphase separation in non-conserved active mixtures

Non-equilibrium phase separating systems with reactions, such as biomolecular condensates and bacteria colonies, can break time-reversal symmetry (TRS) in two distinct ways. Firstly, the conservative and non-conservative sectors of the dynamics can be governed by incompatible free energies; when both sectors are present, this is the leading-order TRS violation, captured in its simplest form by ‘Model AB’. Second, the diffusive dynamics can break TRS in its own right. This happens only at higher order in the gradient expansion (but is the leading behaviour without reactions present) and is captured by ‘Active Model B+’ (AMB+). Each of the two mechanisms can lead to microphase separation, by quite different routes. Here we introduce Model AB+, for which both mechanisms are simultaneously present, and show that for slow reaction rates the system can undergo a new type of hierarchical microphase separation, which we call ‘bubbly microphase separation’. In this state, small droplets of one fluid are continuously created and absorbed into large droplets, whose length-scales are controlled by the competing reactive and diffusive dynamics.

Transcending Conventional Biometry Frontiers: Diffusive Dynamics PPG Biometry

This paper presents the first photoplethysmographic (PPG) signal dynamic-based biometric authentication system with a Siamese convolutional neural network (CNN). Our method extracts the PPG signal’s biometric characteristics from its diffusive dynamics, characterized by geometric patterns in the (p,q)-planes specific to the 0–1 test. PPG signal diffusive dynamics are strongly dependent on the vascular bed’s biostructure, unique to each individual. The dynamic characteristics of the PPG signal are more stable over time than its morphological features, particularly in the presence of psychosomatic conditions. Besides its robustness, our biometric method is anti-spoofing, given the complex nature of the blood network. Our proposal trains using a national research study database with 40 real-world PPG signals measured with commercial equipment. Biometric system results for input data, raw and preprocessed, are studied and compared with eight primary biometric methods related to PPG, achieving the best equal error rate (ERR) and processing times with a single attempt, among all of them.

Experimental demonstration of the novel “van-Hove integral method (vHI)” for measuring diffusive dynamics by elastic neutron scattering

Quasi-elastic neutron scattering (QENS)—based on the seminal work of Nobel Laureate Brockhouse—has been one of the major methods for studying pico-second to nano-second diffusive dynamics over the past 70 years. This is regarded as an “inelastic” method for dynamics. In contrast, we recently proposed a new neutron-scattering method for dynamics, which uses the elastic line of the scattering to access system dynamics directly in the time domain (Benedetto and Kearley in Sci Rep 9:11284, 2019). This new method has been denoted “vHI” that stands for “van Hove Integral”. The reason is that, under certain conditions, the measured elastic intensity corresponds to the running-time integral of the intermediate scattering function, $$I\left( {Q,t} \right)$$ I Q , t , up to a time that is inversely proportional to the energy band-width incident on the sample. As a result, $$I\left( {Q,t} \right)$$ I Q , t is accessed from the time derivative of the measured vHI profile. vHI has been supported by numerical and Monte-Carlo simulations, but has been difficult to validate experimentally due to the lack of a suitable instrument. Here we show that vHI works in practice, which we achieved by using a simple modification to the standard QENS backscattering spectrometer methodology. Basically, we varied the neutron-energy band-widths incident at the sample via a step-wise variation of the frequency of the monochromator Doppler-drive. This provides a measurement of the vHI profile at the detectors. The same instrument and sample were also used in standard QENS mode for comparison. The intermediate scattering functions, $$I\left( {Q,t} \right)$$ I Q , t , obtained by the two methods—vHI and QENS—are strikingly similar providing a direct experimental validation of the vHI method. Perhaps surprisingly, the counting statistics of the two methods are comparable even though the instrument used was expressly designed for QENS. This shows that the methodology modification adopted here can be used in practice to access vHI profiles at many of the backscattering spectrometers worldwide. We also show that partial integrations of the measured QENS spectrum cannot provide the vHI profile, which clarifies a common misconception. At the same time, we show a novel approach which does access $$I\left( {Q,t} \right)$$ I Q , t from QENS spectra.

Nucleation and Post-Nucleation Growth in Diffusion-Controlled and Hydrodynamic Theory of Solidification

Two-step nucleation and subsequent growth processes were investigated in the framework of the single mode phase-field crystal model combined with diffusive dynamics (corresponding to colloid suspensions) and hydrodynamical density relaxation (simple liquids). It is found that independently of dynamics, nucleation starts with the formation of solid precursor clusters that consist of domains with noncrystalline ordering (ringlike projections are seen from certain angles), and regions that have amorphous structure. Using the average bond order parameter q¯6, we distinguished amorphous, medium range crystallike order (MRCO), and crystalline local orders. We show that crystallization to the stable body-centered cubic phase is preceded by the formation of a mixture of amorphous and MRCO structures. We have determined the time dependence of the phase composition of the forming solid state. We also investigated the time/size dependence of the growth rate for solidification. The bond order analysis indicates similar structural transitions during solidification in the case of diffusive and hydrodynamic density relaxation.

Quantitative Theory for the Diffusive Dynamics of Liquid Condensates

To unravel the biological functions of membraneless liquid condensates it is crucial to develop a quantitative understanding of the physics underlying their dynamics. Key processes within such condensates are diffusion and material exchange with their environment. Experimentally, diffusive dynamics are typically probed via fluorescent labels. However, to date we lack a physics-based quantitative framework for the dynamics of labeled condensate components. Here, we derive the corresponding theory, building on the physics of phase separation, and quantitatively validate this framework via experiments. We show that using our theory we can precisely determine diffusion coefficients inside liquid condensates via a spatio-temporal analysis of fluorescence recovery after photobleaching (FRAP) experiments. We showcase the accuracy and precision of our approach by considering space- and time-resolved data of protein condensates and two different polyelectrolyte-coacervate systems. Strikingly, our theory can also be used to determine the diffusion coefficient in the dilute phase and the partition coefficient, without relying on fluorescence measurements in the dilute phase. This bypasses recently described quenching artefacts in the dense phase, which can underestimate partition coefficients by orders of magnitude. Our experimentally verified theory opens new avenues for theoretically describing molecule dynamics in condensates, measuring concentrations based on the dynamics of fluorescence intensities and quantifying rates of biochemical reactions in liquid condensates.