Ordered Assembly of DNA on Topological Insulator Bi2Se3 and Octadecylamine for a Sensitive Biosensor.

Controlling the assembly of DNA in order on a suitable electrode surface is of great significance for biosensors and disease diagnosis, but it is full of challenges. In this work, we creatively assembled DNA on the surface of octadecylamine (ODA)-modified topological insulator (Tls) Bi2Se3 and developed an electrochemical biosensor to detect biomarker DNA of coronavirus disease 2019 (COVID-19). A high-quality Bi2Se3 sheet was obtained from a single crystal synthesized in our lab. A uniform ODA layer was coated in argon by chemical vapor deposition (CVD). We observed and analyzed the assembly and mechanism of single-strand DNA (ssDNA) and double-strand DNA (dsDNA) on the Bi2Se3 surface through atomic force microscopy (AFM) and molecular dynamics (MD) simulations. The electrochemical signal revealed that the biosensor based on the DNA/ODA/Bi2Se3 electrode has a wide linear detection range from 1.0 × 10-12 to 1.0 × 10-8 M, with the limit of detection as low as 5 × 10-13 M. Bi2Se3 has robust surface states and improves the electrochemical signal-to-noise ratio, while the uniform ODA layer guides high-density ordered DNA, enhancing the sensitivity of the biosensor. Our work demonstrates that the ordered DNA/ODA/Bi2Se3 electrode surface has great application potential in the field of biosensing and disease diagnosis.

Thermodynamic nonequilibrium effects in bubble coalescence: A discrete Boltzmann study.

The thermodynamic nonequilibrium (TNE) effects in a coalescence process of two initially static bubbles under thermal conditions are investigated by a discrete Boltzmann model. The spatial distributions of the typical nonequilibrium quantity, i.e., nonorganized momentum fluxes (NOMFs), during evolutions are investigated in detail. The density-weighted statistical method is used to highlight the relationship between the TNE effects and the morphological and kinetics characteristics of bubble coalescence. The results show that the xx component and yy component of NOMFs are antisymmetrical; the xy component changes from an antisymmetric internal and external double quadrupole structure to an outer octupole structure during the coalescence process. Moreover, the evolution of the averaged xx component of NOMFs provides two characteristic instants, which divide the nonequilibrium process into three stages. The first instant, when the averaged xx component of the NOMFs reaches its first local minimum, corresponds to the moment when the mean coalescence speed gets the maximum, and at this time the ratio of minor and major axes is about 1/2. The second instant, when the averaged xx component of the NOMFs gets its second local maximum, corresponds to the moment when the ratio of minor and major axes becomes 1 for the first time. It is interesting to find that the three quantities, TNE intensity, acceleration of coalescence, and the slope of boundary length, show a high degree of correlation and attain their maxima simultaneously. The surface tension and the heat conduction accelerate the process of bubble coalescence, while the viscosity delays it. Both the surface tension and the viscosity enhance the global nonequilibrium intensity, whereas the heat conduction restrains it. These TNE features and findings present some insights into the kinetics of bubble coalescence.

Computational imaging of moving objects obscured by a random corridor via speckle correlations.

Computational imaging makes it possible to reconstruct hidden objects through random media and around corners, which is of fundamental importance in various fields. Despite recent advances, computational imaging has not been studied in certain types of random scenarios, such as tortuous corridors filled with random media. We refer to this category of complex environment as a 'random corridor', and propose a reduced spatial- and ensemble-speckle intensity correlation (RSESIC) method to image a moving object obscured by a random corridor. Experimental results show that the method can reconstruct the image of a centimeter-sized hidden object with a sub-millimeter resolution by a low-cost digital camera. The imaging capability depends on three system parameters and can be characterized by the correlation fidelity (CF). Furthermore, the RSESIC method is able to recover the image of objects even for a single pixel containing the contribution of about 102 speckle grains, which overcomes the theoretical limitation of traditional speckle imaging methods. Last but not least, when the power attenuation of speckle intensity leads to serious deterioration of CF, the image of hidden objects can still be reconstructed by the corrected intensity correlation.

Spontaneous population oscillation of confined active granular particles.

Spontaneous collective oscillation may emerge from seemingly irregular active matter systems. Here, we experimentally demonstrate a spontaneous population oscillation of active granular particles confined in two chambers connected by a narrow channel, and verify the intriguing behavior predicted in simulation [M. Paoluzzi, R. Di Leonardo and L. Angelani, Self-sustained density oscillations of swimming bacteria confined in microchambers, Phys. Rev. Lett., 2015, 115(18), 188303]. During the oscillation, the two chambers are alternately (nearly) filled up and emptied by the self-propelled particles in a periodic manner. We show that the stable unidirectional flow induced due to the confined channel and its periodic reversal triggered by the particle concentration difference between two chambers jointly give rise to the oscillatory collective behavior. Furthermore, we propose a minimal theoretical model that properly reproduces the experimental results without free parameters. This self-sustained collective oscillation could serve as a robust active granular clock, capable of providing rhythmic signals.

Electrochemical biosensor based on topological insulator Bi2Se3 tape electrode for HIV-1 DNA detection.

A large-size Bi2Se3 tape electrode (BTE) was prepared by peeling off a 2 × 1 × 0.5 cm high-quality single crystal. The feasibility of using the flexible BTE as an efficient bioplatform to load Au nanoparticles and probe DNA for HIV-1 DNA electrochemical sensing was explored. Differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS) show that the resultant biosensor has a wide linear range from 0.1 fM to 1 pM, a low detection limit of 50 aM, excellent selectivity, reproducibility and stability, and is superior to the pM DNA detection level of Pt-Au, graphene-AuNPs hybrid biosensors. This outstanding performance is attributed to the intrinsic surface state of Bi2Se3 topological insulator in facilitating electron transfer. Therefore, BTE electrochemical biosensor platform has great potential in the application for sensitive detection of DNA biomarkers.

Clogging of granular materials in a horizontal hopper: Effect of outlet size, hopper angle, and driving velocity.

Due to the independence of the driving velocity and outlet size, it is possible to isolate geometrical and kinematic contributions to clogging in two-dimensional horizontal flow in a hopper driven by a conveyor belt. We experimentally investigate the geometric (outlet size and hopper angle) and kinematic effects (driving velocity) on the clogging in such a horizontal flow. Based on quantitative measurements and analysis of the avalanche size, blocking probability of a particle at the outlet, and other parameters, we show that the geometric factors can more effectively affect clogging. In addition, we find that the clogging tends to be alleviated with the increases of the driving velocity, suggesting a possible "fast is fast" behavior within a wide range of driving velocity. We borrow and modify a model from clogging in gravity-driven hoppers, which can accurately describe the shape of the clogging probability function in the conveyor belt driven flow, suggesting that these two systems could share some mechanisms for clogging.

Topologically Protected Transport of Cargo in a Chiral Active Fluid Aided by Odd-Viscosity-Enhanced Depletion Interactions.

The discovery of topological edge states that unidirectionally propagate along the boundary of system without backscattering has enabled the development of new design principles for material or information transport. Here, we show that the topological edge flow supported by the chiral active fluid composed of spinners can even robustly transport an immersed intruder with the aid of the spinner-mediated depletion interaction between the intruder and boundary. Importantly, the effective interaction significantly depends on the dissipationless odd viscosity of the chiral active fluid, which originates from the spinning-induced breaking of time-reversal and parity symmetries, rendering the transport controllable. Our findings propose a novel avenue for robust cargo transport and could open a range of new possibilities throughout biological and microfluidic systems.

DNA rearrangement on the octadecylamine modified graphite surface by heating and ultrasonic treatment.

The evolution of single-stranded DNA (ssDNA) assembly on octadecylamine (ODA) modified highly oriented pyrolytic graphite (HOPG) surface by heating and ultrasonic treatment has been studied for the first time. We have observed that DNA on the ODA coated HOPG surface underwent dramatic morphological changes as a function of heating and ultrasonic treatment. Ordered DNA firstly changed to random aggregates by heating and then changed to three-dimensional (3D) networks by ultrasonic treatment. This finding points to previously unknown factors that impact graphite-DNA interaction and opens new opportunities to control the deposition of DNA onto graphitic substrates. In this way, we built a cost-effective method to produce large-scale 3D ssDNA networks. All of these studies pave the way to understand the properties of DNA-solid interface, design novel nanomaterials, and improve the sensitivity of DNA biosensors.

Simultaneous Multiplexed Detection of Protein and Metal Ions by a Colorimetric Microfluidic Paper-based Analytical Device.

In order to improve the efficiency of disease diagnosis and environmental monitoring, it is desirable to detect the concentration of proteins and metal ions simultaneously, since the current popular diagnostic platform can only detect proteins or metal ions independently. In this work, we developed a colorimetric microfluidic paper-based analytical device (µPAD) for simultaneous determination of protein (bovine serum albumin, BSA) and metal ions [Fe(III) and Ni(II)]. The µPAD consisted of one central zone, ten reaction zones and ten detection zones in one device, in which reaction solutions were effectively optimized for different types of chromogenic reactions. Fe(III), Ni(II) and BSA can be easily identified by the colored products, and their concentrations are in good accordance with color depth based on the established standard curves. The detection limits are 0.1 mM for Fe(III), 0.5 mM for Ni(II) and 1µM for BSA, respectively. Best of all, we demonstrated the efficiency of the µPAD with accurate detection of Fe(III), Ni (II) and BSA from river water samples within 15 minutes. The µPAD detection is efficient, instrument-free, and easy-to-use, holding great potential for simultaneous detection of cross type analytes in numerous diagnostic fields.

Flux of granular particles through a shaken sieve plate.

We experimentally investigate a discharging flux of granular particles through a sieve plate subject to vertical vibrations. The mean mass flux shows a non-monotonic relation with the vibration strength. High-speed photography reveals that two stages, the free flight of the particles' bulk over the plate and the adhesion of the particles' bulk with the plate, alternately appear, where only the adhesion stage contributes to the flow. With two independent methods, we then measure the adhesion time under different vibration conditions, and define an adhesion flux. The adhesion flux monotonically increases with increasing vibration strength. By rescaling the adhesion flux, we find that the adhesion flux is approximately determined by the peak vibration velocity of the shaker. The conclusion is examined with other sieve geometries.

Symmetrically periodic segregation in a vertically vibrated binary granular bed.

Periodic segregation behaviors in fine mixtures of copper and alumina particles, including both percolation and eruption stages, are experimentally investigated by varying the ambient air pressure and vibrational acceleration. For the cases with moderate air pressure, the heaping profile of the granular bed keeps symmetrical in the whole periodic segregation. The symmetrical shape of the upper surface of the granular bed in the eruption stage, which resembles a miniature volcanic eruption, could be described by the Mogi model that illuminates the genuine volcanic eruption in the geography. When the air pressure increases, an asymmetrical heaping profile is observed in the eruption stage of periodic segregation. With using the image processing technique, we estimate a relative height difference between the copper and the alumina particles as the order parameter to quantitatively characterize the evolution of periodic segregation. Both eruption and percolation time, extracted from the order parameter, are plotted as a function of the vibration strength. Finally, we briefly discuss the air effect on the granular segregation behaviors.

Segregation in mixtures of granular chains and spherical grains under vertical vibration.

We experimentally investigate segregation behaviors of binary granular mixtures consisting of granular chains and spherical grains with different interstitial media under vertical vibrations. A quantitative criterion is proposed to locate the boundaries between different vibrating phases. The water-immersed granular mixture exhibits two interesting types of segregation behaviors: chain-on-top and sandwich patterns. However, the phenomenon of sandwich segregation is absent for the air-immersed mixture. The topological differences of phase diagrams between two different environments indicate that the interstitial fluid plays an important role on the granular demixing. Additionally, the phase behaviors of mixtures for the different chain lengths show a not significant discrepancy. Finally, the vibrating thickness ratio determining the phase boundary characterizes the mixing extent of the granular bed. The estimated ratios for various chain lengths exhibit a monotonically decreasing dependence, when the vibration frequency increases.

Polymerlike statistical characterization of two-dimensional granular chains.

Statistical behaviors of packing collections of granular chains in a two-dimensional container have been investigated experimentally. On compaction from their own gravity, the longer chains pack into a structure with lower packing density due to the prevalence of backbone loops. The packing of chains can be considered as the jamming of the granular system. The structure factor of packing chains shows scaling behavior g(q)∼q(-2) in good agreement with dense polymer solutions. In addition, we compute various probability distributions of distances and estimate three crucial contact exponents, finding that the scaling behavior from granular chains is in accord with the theoretical expectation of polymers. Finally, an orientational anticorrelation of granular chains is observed by bond-bond correlation function, which agrees with the results in the two-dimensional model of compact polymers.

Percolation current in a periodic segregation of a binary granular mixture.

A periodic segregation in a binary granular mixture of alumina and copper spheres has been found when the mixture is subjected to vertical vibrations, in which a stable percolation process has been experimentally studied. Measurements reveal that the percolation time of alumina particles through a permeable layer of copper particles increases linearly as the number of alumina particles increases. While the percolation current of alumina particles proves to be independent of the number of alumina particles, it shows a monotonically decreasing relationship with the number of copper particles in the mixture. Finally, we briefly discuss possible candidates to affect the percolation current.