Quantifying RNA structures and interactions with a unified reduced chain representation model.

RNA is a pivotal molecule that plays critical roles in various cellular processes. Quantifying RNA structures and interactions is essential to understanding RNA function and developing RNA-based therapeutics. Using a unified five-bead model and a non-redundant database, this paper investigates the structural features and interactions of five commonly occurring RNA motifs, i.e., double-stranded helices, hairpin loops, internal/bulge loops, multi-branched junctions, and single-stranded terminal tails. Analyzing detailed distributions of RNA local structural features and base-base interactions reveals a preference for helical structures in both local backbone structures and base orientations. The interactions between adjacent bases exhibit motif-specific and sequence-dependent characteristics, reflecting the distinct topological constraints imposed by different loop-helix connection modes and the varying pairing and stacking interactions among different sequences. These findings shed light on the stability of RNA helices, emphasizing their significance in providing dominant base pairing and stacking interactions for RNA structures and stability. The four non-helix motifs encompass unpaired nucleotide loops and exhibit diverse base-base interactions, contributing to the structural diversity observed in RNA. Overall, the complexity of RNA structure arises from the intricate interplay of base-base interactions.

Ultra-Wideband High-Efficiency Solar Absorber and Thermal Emitter Based on Semiconductor InAs Microstructures.

Since the use of chemical fuels is permanently damaging the environment, the need for new energy sources is urgent for mankind. Given that solar energy is a clean and sustainable energy source, this study investigates and proposes a six-layer composite ultra-wideband high-efficiency solar absorber with an annular microstructure. It achieves this by using a combination of the properties of metamaterials and the quantum confinement effects of semiconductor materials. The substrate is W-Ti-Al2O3, and the microstructure is an annular InAs-square InAs film-Ti film combination. We used Lumerical Solutions' FDTD solution program to simulate the absorber and calculate the model's absorption, field distribution, and thermal radiation efficiency (when it is used as a thermal emitter), and further explored the physical mechanism of the model's ultra-broadband absorption. Our model has an average absorption of 95.80% in the 283-3615 nm band, 95.66% in the 280-4000 nm band, and a weighted average absorption efficiency of 95.78% under AM1.5 illumination. Meanwhile, the reflectance of the model in the 5586-20,000 nm band is all higher than 80%, with an average reflectance of 94.52%, which has a good thermal infrared suppression performance. It is 95.42% under thermal radiation at 1000 K. It has outstanding performance when employed as a thermal emitter as well. Additionally, simulation results show that the absorber has good polarization and incidence angle insensitivity. The model may be applied to photodetection, thermophotovoltaics, bio-detection, imaging, thermal ion emission, and solar water evaporation for water purification.

Mutual effects between single-stranded DNA conformation and Na+-Mg2+ ion competition in mixed salt solutions.

The ion-dependence of single-stranded DNA (ssDNA) conformational changes has attracted growing attention because of its biological and technological importance. Although single-species ion effects have been extensively explored, it is challenging to study the ssDNA conformational properties under mixed monovalent/divalent ion conditions due to the complications of ssDNA flexibility and ion-ion competition. In this study, we apply Langevin dynamics simulations to investigate mixed Na+/Mg2+ ion-dependent ssDNA conformations. The ssDNA structure is described using a coarse-grained model, in which the phosphate, base, and sugar of each nucleotide are represented by three different beads. A novel improvement in our simulation model is that mixed-salt-related electrostatic interactions are computed via combining Manning counterion condensation (MCC) theory with the Monte Carlo tightly bound ion (MCTBI) model. Based on this MCC-MCTBI combination, we report new empirical functions to describe the ion-concentration-dependent and ssDNA conformation/structure-dependent electrostatic effects. The calculation results relating to the ion binding properties and the simulation results relating to the ssDNA conformational properties are validated against experimental results. In addition, our simulation results suggest a quantitative relationship between the ssDNA conformation and Na+-Mg2+ competition; this in turn reveals their mutual impact in the ion atmosphere.

The Light Absorption Enhancement in Graphene Monolayer Resulting from the Diffraction Coupling of Surface Plasmon Polariton Resonance.

In this study, we investigate a physical mechanism to improve the light absorption efficiency of graphene monolayer from the universal value of 2.3% to about 30% in the visible and near-infrared wavelength range. The physical mechanism is based on the diffraction coupling of surface plasmon polariton resonances in the periodic array of metal nanoparticles. Through the physical mechanism, the electric fields on the surface of graphene monolayer are considerably enhanced. Therefore, the light absorption efficiency of graphene monolayer is greatly improved. To further confirm the physical mechanism, we use an interaction model of double oscillators to explain the positions of the absorption peaks for different array periods. Furthermore, we discuss in detail the emerging conditions of the diffraction coupling of surface plasmon polariton resonances. The results will be beneficial for the design of graphene-based photoelectric devices.

Theoretical Study on Metasurfaces for Transverse Magneto-Optical Kerr Effect Enhancement of Ultra-Thin Magnetic Dielectric Films.

We study how to enhance the transverse magneto-optical Kerr effect (TMOKE) of ultra-thin magnetic dielectric films through the excitation of strong magnetic resonances on metasurface with a metal nanowire array stacked above a metal substrate with an ultra-thin magnetic dielectric film spacer. The plasmonic hybridizations between the Au nanowires and substrate result in magnetic resonances. The periodic arrangement of the Au nanowires can excite propagating surface plasmon polaritons (SPPs) on the metal surface. When the SPPs and the magnetic resonances hybridize, they can strongly couple to form two strong magnetic resonances, which are explained by a coupled oscillator model. Importantly, benefitting from the strong magnetic resonances, we can achieve a large TMOKE signal up to 26% in the ultra-thin magnetic dielectric film with a thickness of only 30 nm, which may find potential applications in nanophotonics, magnonics, and spintronics.

Pronounced Linewidth Narrowing of Vertical Metallic Split-Ring Resonators via Strong Coupling with Metal Surface.

We theoretically study the plasmonic coupling between magnetic plasmon resonances (MPRs) and propagating surface plasmon polaritons (SPPs) in a three-dimensional (3D) metamaterial consisting of vertical Au split-ring resonators (VSRRs) array on Au substrate. By placing the VSRRs directly onto the Au substrate to remove the dielectric substrates effect, the interaction between MPRs of VSRRs and the SPP mode on the Au substrate can generate an ultranarrow-band hybrid mode with full width at half maximum (FWHM) of 2.2 nm and significantly enhanced magnetic fields, compared to that of VSRRs on dielectric substrates. Owing to the strong coupling, an anti-crossing effect similar to Rabi splitting in atomic physics is also obtained. Our proposed 3D metamaterial on a metal substrate shows high sensitivity (S = 830 nm/RIU) and figure of merit (FOM = 377), which could pave way for the label-free biomedical sensing.

Ultraviolet graphene ultranarrow absorption engineered by lattice plasmon resonance.

We numerically demonstrate an ultraviolet graphene ultranarrow absorption in a hybrid graphene-metal structure. The full-width at half maximum of the absorption band being 9 nm in ultraviolet range is achieved based on the coupling of lattice plasmon resonances of the metallic nanostructure to the optical dissipation of graphene. The position, absorbance and linewidth of the hybridized narrow resonant mode tuned by controlling geometrical parameters and materials are systematically investigated. The proposed structure possesses high refractive index sensitivity of 288 nm/RIU and figure of merit of 72, and can also be used to detect small molecules layer of sub-nanometer thickness and refractive index with small changes, providing promising applications in ultra-compact efficient biosensors.

Multipolar Plasmonic Resonances of Aluminum Nanoantenna Tuned by Graphene.

We numerically investigate the multipolar plasmonic resonances of Aluminum nanoantenna tuned by a monolayer graphene from ultraviolet (UV) to visible regime. It is shown that the absorbance of the plasmonic odd modes (l = 1 and l = 3) of graphene-Al nanoribbon structure is enhanced while the absorption at the plasmonic even modes (l = 2) is suppressed, compared to the pure Al nanoribbon structure. With the presence of the monolayer graphene, a change in the resonance strength of the multipolar plasmonic modes results from the near field interactions of the monolayer graphene with the electric fields of the multipolar plasmonic resonances of the Al resonator. In particular, a clear absorption peak with a high quality (Q)-factor of 27 of the plasmonic third-order mode (l = 3) is realized in the graphene-Al nanoribbon structure. The sensitivity and figure of merit of the plasmonic third-order mode of the proposed Graphene-Al nanoribbon structure can reach 25 nm/RIU and 3, respectively, providing potential applications in optical refractive-index sensing.

Narrowband Light Reflection Resonances from Waveguide Modes for High-Quality Sensors.

Designing various nanostructures to achieve narrowband light reflection resonances is desirable for optical sensing applications. In this work, we theoretically demonstrate two narrowband light reflection resonances resulting from the excitations of the zero-order transverse magnetic (TM) and transverse electric (TE) waveguide modes, in a waveguide structure consisting of an Au sphere array on an indium tin oxide (ITO) spacer on a silica (SiO2) substrate. The positions of the light reflection resonances can be tuned easily, by varying the array periods of gold (Au) spheres or by changing the thickness of the ITO film. More importantly, the light reflection resonances have a very narrow bandwidth, the full width at half maximum (FWHM) of which can be reduced to only several nanometers for the zero-order TM and TE waveguide modes. The conventionally defined performance parameters of sensors, sensitivity (S) and figure of merit (FOM), have quite high values of about 80 nm/RIU and 32, respectively, in the visible wavelength range.

Anisotropic Transport and Quantum Oscillations in the Quasi-One-Dimensional TaNiTe5: Evidence for the Nontrivial Band Topology.

The past decade has witnessed the burgeoning discovery of a variety of topological states of matter with distinct nontrivial band topologies. Thus far, most materials that have been studied possess two-dimensional or three-dimensional electronic structures, with only a few exceptions that host quasi-one-dimensional (quasi-1D) topological electronic properties. Here we present clear-cut evidence for Dirac Fermions in the quasi-1D telluride TaNiTe5. We show that its transport behaviors are highly anisotropic, and we observe nontrivial Berry phases via quantum oscillation measurements. The nontrivial band topology is further corroborated by first-principles calculations. Our results may help to guide the future quest for topological states in this new family of quasi-1D ternary chalcogenides.

Kinetic Mechanism of RNA Helix-Terminal Basepairing-A Kinetic Minima Network Analysis.

RNA functions are often kinetically controlled. The folding kinetics of RNAs involves global structural changes and local nucleotide movement, such as base flipping. The most elementary step in RNA folding is the closing and opening of a basepair. By integrating molecular dynamics simulation, master equation, and kinetic Monte Carlo simulation, we investigate the kinetics mechanism of RNA helix-terminal basepairing. The study reveals a six-state folding scheme with three dominant folding pathways of tens, hundreds, and thousands of nanoseconds of folding timescales, respectively. The overall kinetics is rate limited by the detrapping of a misfolded state with the overall folding time of 10-5 s. Moreover, the analysis examines the different roles of the various driving forces, such as the basepairing and stacking interactions and the ion binding/dissociation effects on structural changes. The results may provide useful insights for developing a basepair opening/closing rate model and further kinetics models of large RNAs.

The study on size dependent dipole-dipole interaction in the self-assembly of twisting nanoribbons with circular polarization activation.

The mechanism of self-assembling process of inorganic nanoparticle (NPs) is still an open question due to the various and non-additive interactions between NPs. Kotov et al reported that the semiconductor NPs can be self-assembled by external activation such as irradiation. In this paper, the twisted CdTe nanoribbons were successfully assembled with circular polar light activation based on the chiral selective resonance absorption. The effect of NP size on the morphology of assemblies under circular polar light irradiation is discussed by introducing a new mechanism of photooxidation induced dipole moment which decreases with increasing sizes of the NPs because of the change of band offsets at the CdS/CdTe interface. Moreover, we find that the competition between the dipole-dipole interaction and electrostatic repulsion can be modulated by the size of the NPs and the concentration of dispersion, which are the key points to produce the chiral twisted nanoribbons.

Chirality-dependent electromagnetically induced transparency based on a double semi-periodic helix metastructure.

A chiral metastructure composed of spatially separated double semi-periodic helices is proposed and investigated theoretically and experimentally in this Letter. Chirality-dependent electromagnetically induced transparency (EIT) and a slow light effect in the microwave region are observed from a numerical parameter study, while experimental results from the 3D printing sample yield good agreement with the theoretical findings. The studied EIT phenomenon arises as a result of destructive interference by coupled resonances, and the proposed chiral metastructure can be applied in areas such as polarization communication, pump-probe characterization, and quantum computing areas.

Surface enhanced Raman scattering substrates prepared by thermal evaporation on liquid surfaces.

We present an effective surface-enhancement Raman scattering (SERS) substrate enabled by depositing metallic film on a liquid surface at room temperature. Thermal evaporation is used to deposit Au atoms on silicone oil surface and then form quasi-continuous films. Due to the isotropic characteristics of the liquid surface, this film consists of substantial nanoparticles with uniform diameter, which is different from films fabricated on solid substrates and can be served as an applicable substrate for SERS detection. With the assistance of this substrate, SERS signals of rhodamine 6G were significantly enhanced, the dependence between SERS spectra and film thickness was investigated. Analytical simulation results confirm the experimental observations and the superiorities of our proposed method for preparation of SERS substrate. This work provides a potential application of metallic film deposition on free-sustained surface and holds promise as an efficient sensor in rapid trace detection of small molecule analytes.

Temporal Variation in Single-Cell Power-Law Rheology Spans the Ensemble Variation of Cell Population.

Changes in the cytoskeletal organization within cells can be characterized by large spatial and temporal variations in rheological properties of the cell (e.g., the complex shear modulus G∗). Although the ensemble variation in G∗ of single cells has been elucidated, the detailed temporal variation of G∗ remains unknown. In this study, we investigated how the rheological properties of individual fibroblast cells change under a spatially confined environment in which the cell translational motion is highly restricted and the whole cell shape remains unchanged. The temporal evolution of single-cell rheology was probed at the same measurement location within the cell, using atomic force microscopy-based oscillatory deformation. The measurements reveal that the temporal variation in the power-law rheology of cells is quantitatively consistent with the ensemble variation, indicating that the cell system satisfies an ergodic hypothesis in which the temporal statistics are identical to the ensemble statistics. The autocorrelation of G∗ implies that the cell mechanical state evolves in the ensemble of possible states with a characteristic timescale.

Phase shifting mask modulated laser patterning on graphene.

A one-step graphene patterning method is developed in this paper. A phase shifting mask is used to modulate incident laser beam spatially and generate graphene patterns by laser heating. Periodic graphene nanoribbon and nanomesh structures are fabricated by employing 1D and 2D phase shifting masks, respectively. The noncontact, simple procedure, easy handling and economic properties of this method make it promising towards graphene-based device fabrication.

Quantifying cell-to-cell variation in power-law rheology.

Among individual cells of the same source and type, the complex shear modulus G(∗) exhibits a large log-normal distribution that is the result of spatial, temporal, and intrinsic variations. Such large distributions complicate the statistical evaluation of pharmacological treatments and the comparison of different cell states. However, little is known about the characteristic features of cell-to-cell variation. In this study, we investigated how this variation depends on the spatial location within the cell and on the actin filament cytoskeleton, the organization of which strongly influences cell mechanics. By mechanically probing fibroblasts arranged on a microarray, via atomic force microscopy, we observed that the standard deviation σ of G(∗) was significantly reduced among cells in which actin filaments were depolymerized. The parameter σ also exhibited a subcellular spatial dependence. Based on our findings regarding the frequency dependence of σ of the storage modulus G('), we proposed two types of cell-to-cell variation in G(') that arise from the purely elastic and the frequency-dependent components in terms of the soft glassy rheology model of cell deformability. We concluded that the latter inherent cell-to-cell variation can be reduced greatly by disrupting actin networks, by probing at locations within the cell nucleus boundaries distant from the cell center, and by measuring at high loading frequencies.