Accurate virus identification with interpretable Raman signatures by machine learning.

Rapid identification of newly emerging or circulating viruses is an important first step toward managing the public health response to potential outbreaks. A portable virus capture device, coupled with label-free Raman spectroscopy, holds the promise of fast detection by rapidly obtaining the Raman signature of a virus followed by a machine learning (ML) approach applied to recognize the virus based on its Raman spectrum, which is used as a fingerprint. We present such an ML approach for analyzing Raman spectra of human and avian viruses. A convolutional neural network (CNN) classifier specifically designed for spectral data achieves very high accuracy for a variety of virus type or subtype identification tasks. In particular, it achieves 99% accuracy for classifying influenza virus type A versus type B, 96% accuracy for classifying four subtypes of influenza A, 95% accuracy for differentiating enveloped and nonenveloped viruses, and 99% accuracy for differentiating avian coronavirus (infectious bronchitis virus [IBV]) from other avian viruses. Furthermore, interpretation of neural net responses in the trained CNN model using a full-gradient algorithm highlights Raman spectral ranges that are most important to virus identification. By correlating ML-selected salient Raman ranges with the signature ranges of known biomolecules and chemical functional groups­for example, amide, amino acid, and carboxylic acid­we verify that our ML model effectively recognizes the Raman signatures of proteins, lipids, and other vital functional groups present in different viruses and uses a weighted combination of these signatures to identify viruses.

Designing artificial two-dimensional landscapes via atomic-layer substitution.

Technology advancements in history have often been propelled by material innovations. In recent years, two-dimensional (2D) materials have attracted substantial interest as an ideal platform to construct atomic-level material architectures. In this work, we design a reaction pathway steered in a very different energy landscape, in contrast to typical thermal chemical vapor deposition method in high temperature, to enable room-temperature atomic-layer substitution (RT-ALS). First-principle calculations elucidate how the RT-ALS process is overall exothermic in energy and only has a small reaction barrier, facilitating the reaction to occur at room temperature. As a result, a variety of Janus monolayer transition metal dichalcogenides with vertical dipole could be universally realized. In particular, the RT-ALS strategy can be combined with lithography and flip-transfer to enable programmable in-plane multiheterostructures with different out-of-plane crystal symmetry and electric polarization. Various characterizations have confirmed the fidelity of the precise single atomic layer conversion. Our approach for designing an artificial 2D landscape at selective locations of a single layer of atoms can lead to unique electronic, photonic, and mechanical properties previously not found in nature. This opens a new paradigm for future material design, enabling structures and properties for unexplored territories.

Engineered 2D materials for optical bioimaging and path toward therapy and tissue engineering.

Two-dimensional (2D) layered materials as a new class of nanomaterial are characterized by a list of exotic properties. These layered materials are investigated widely in several biomedical applications. A comprehensive understanding of the state-of-the-art developments of 2D materials designed for multiple nanoplatforms will aid researchers in various fields to broaden the scope of biomedical applications. Here, we review the advances in 2D material-based biomedical applications. First, we introduce the classification and properties of 2D materials. Next, we summarize surface and structural engineering methods of 2D materials where we discuss surface functionalization, defect, and strain engineering, and creating heterostructures based on layered materials for biomedical applications. After that, we discuss different biomedical applications. Then, we briefly introduced the emerging role of machine learning (ML) as a technological advancement to boost biomedical platforms. Finally, the current challenges, opportunities, and prospects on 2D materials in biomedical applications are discussed.

Signature of Many-Body Localization of Phonons in Strongly Disordered Superlattices.

Many-body localization (MBL) has attracted significant attention because of its immunity to thermalization, role in logarithmic entanglement entropy growth, and opportunities to reach exotic quantum orders. However, experimental realization of MBL in solid-state systems has remained challenging. Here, we report evidence of a possible phonon MBL phase in disordered GaAs/AlAs superlattices. Through grazing-incidence inelastic X-ray scattering, we observe a strong deviation of the phonon population from equilibrium in samples doped with ErAs nanodots at low temperature, signaling a departure from thermalization. This behavior occurs within finite phonon energy and wavevector windows, suggesting a localization-thermalization crossover. We support our observation by proposing a theoretical model for the effective phonon Hamiltonian in disordered superlattices, and showing that it can be mapped exactly to a disordered 1D Bose-Hubbard model with a known MBL phase. Our work provides momentum-resolved experimental evidence of phonon localization, extending the scope of MBL to disordered solid-state systems.

Enhancement of van der Waals Interlayer Coupling through Polar Janus MoSSe.

Interlayer coupling plays essential roles in the quantum transport, polaritonic, and electrochemical properties of stacked van der Waals (vdW) materials. In this work, we report the unconventional interlayer coupling in vdW heterostructures (HSs) by utilizing an emerging 2D material, Janus transition metal dichalcogenides (TMDs). In contrast to conventional TMDs, monolayer Janus TMDs have two different chalcogen layers sandwiching the transition metal and thus exhibit broken mirror symmetry and an intrinsic vertical dipole moment. Such a broken symmetry is found to strongly enhance the vdW interlayer coupling by as much as 13.2% when forming MoSSe/MoS2 HS as compared to the pristine MoS2 counterparts. Our noncontact ultralow-frequency Raman probe, linear chain model, and density functional theory calculations confirm the enhancement and reveal the origins as charge redistribution in Janus MoSSe and reduced interlayer distance. Our results uncover the potential of tuning interlayer coupling strength through Janus heterostacking.

Topological Singularity Induced Chiral Kohn Anomaly in a Weyl Semimetal.

The electron-phonon interaction (EPI) is instrumental in a wide variety of phenomena in solid-state physics, such as electrical resistivity in metals, carrier mobility, optical transition, and polaron effects in semiconductors, lifetime of hot carriers, transition temperature in BCS superconductors, and even spin relaxation in diamond nitrogen-vacancy centers for quantum information processing. However, due to the weak EPI strength, most phenomena have focused on electronic properties rather than on phonon properties. One prominent exception is the Kohn anomaly, where phonon softening can emerge when the phonon wave vector nests the Fermi surface of metals. Here we report a new class of Kohn anomaly in a topological Weyl semimetal (WSM), predicted by field-theoretical calculations, and experimentally observed through inelastic x-ray and neutron scattering on WSM tantalum phosphide. Compared to the conventional Kohn anomaly, the Fermi surface in a WSM exhibits multiple topological singularities of Weyl nodes, leading to a distinct nesting condition with chiral selection, a power-law divergence, and non-negligible dynamical effects. Our work brings the concept of the Kohn anomaly into WSMs and sheds light on elucidating the EPI mechanism in emergent topological materials.

Direct Observation of Symmetry-Dependent Electron-Phonon Coupling in Black Phosphorus.

Electron-phonon coupling in two-dimensional nanomaterials plays a fundamental role in determining their physical properties. Such interplay is particularly intriguing in semiconducting black phosphorus (BP) due to the highly anisotropic nature of its electronic structure and phonon dispersions. Here we report the direct observation of symmetry-dependent electron-phonon coupling in BP by performing the polarization-selective resonance Raman measurement in the visible and ultraviolet regimes, focusing on the out-of-plane Ag1 and in-plane Ag2 phonon modes. Their intrinsic resonance Raman excitation profiles (REPs) were extracted and quantitatively compared. The in-plane Ag2 mode exhibits remarkably strong resonance enhancement across the excitation wavelengths when the excitation polarization is parallel to the armchair (Ag2//AC) direction. In contrast, a dramatically weak resonance effect was observed for the same mode with the polarization parallel to zigzag (Ag2//ZZ) direction and for the out-of-plane Ag1 mode (Ag1//AC and Ag1//ZZ). Analysis on quantum perturbation theory and first-principles calculations on the anisotropic electron distributions in BP demonstrated that electron-phonon coupling considering the symmetry of the involved excited states and phonon vibration patterns is responsible for this phenomenon. Further analysis of the polarization-dependent REPs for Ag phonons allows us to resolve the existing controversies on the physical origin of Raman anomaly in BP and its dependence on excitation energy, sample thickness, phonon modes, and crystalline orientation. Our study gives deep insights into the underlying interplay between electrons and phonons in BP and paves the way for manipulating the electron-phonon coupling in anisotropic nanomaterials for future device applications.

Large Photothermal Effect in Sub-40 nm h-BN Nanostructures Patterned Via High-Resolution Ion Beam.

The controlled nanoscale patterning of 2D materials is a promising approach for engineering the optoelectronic, thermal, and mechanical properties of these materials to achieve novel functionalities and devices. Herein, high-resolution patterning of hexagonal boron nitride (h-BN) is demonstrated via both helium and neon ion beams and an optimal dosage range for both ions that serve as a baseline for insulating 2D materials is identified. Through this nanofabrication approach, a grating with a 35 nm pitch, individual structure sizes down to 20 nm, and additional nanostructures created by patterning crystal step edges are demonstrated. Raman spectroscopy is used to study the defects induced by the ion beam patterning and is correlated to scanning probe microscopy. Photothermal and scanning near-field optical microscopy measure the resulting near-field absorption and scattering of the nanostructures. These measurements reveal a large photothermal expansion of nanostructured h-BN that is dependent on the height to width aspect ratio of the nanostructures. This effect is attributed to the large anisotropy of the thermal expansion coefficients of h-BN and the nanostructuring implemented. The photothermal expansion should be present in other van der Waals materials with large anisotropy and can lead to applications such as nanomechanical switches driven by light.

The renaissance of black phosphorus.

One hundred years after its first successful synthesis in the bulk form in 1914, black phosphorus (black P) was recently rediscovered from the perspective of a 2D layered material, attracting tremendous interest from condensed matter physicists, chemists, semiconductor device engineers, and material scientists. Similar to graphite and transition metal dichalcogenides (TMDs), black P has a layered structure but with a unique puckered single-layer geometry. Because the direct electronic band gap of thin film black P can be varied from 0.3 eV to around 2 eV, depending on its film thickness, and because of its high carrier mobility and anisotropic in-plane properties, black P is promising for novel applications in nanoelectronics and nanophotonics different from graphene and TMDs. Black P as a nanomaterial has already attracted much attention from researchers within the past year. Here, we offer our opinions on this emerging material with the goal of motivating and inspiring fellow researchers in the 2D materials community and the broad readership of PNAS to discuss and contribute to this exciting new field. We also give our perspectives on future 2D and thin film black P research directions, aiming to assist researchers coming from a variety of disciplines who are desirous of working in this exciting research field.

Sensitive Phonon-Based Probe for Structure Identification of 1T' MoTe2.

In this work, by combining transmission electron microscopy and polarized Raman spectroscopy for the 1T' MoTe2 flakes with different thicknesses, we found that the polarization dependence of Raman intensity is given as a function of excitation laser wavelength, phonon symmetry, and phonon frequency, but has weak dependence on the flake thickness from few-layer to multilayer. In addition, the frequency of Raman peaks and the relative Raman intensity are sensitive to flake thickness, which manifests Raman spectroscopy as an effective probe for thickness of 1T' MoTe2. Our work demonstrates that polarized Raman spectroscopy is a powerful and nondestructive method to quickly identify the crystal structure and thickness of 1T' MoTe2 simultaneously, which opens up opportunities for the in situ probe of anisotropic properties and broad applications of this novel material.

Black Phosphorus: Optical Characterization, Properties and Applications.

The rise of black phosphorus (BP) as a new family member of two-dimensional (2D) materials brings new concepts and applications to the field, because of the infrared band gap and anisotropic properties of such materials. Among many excellent properties of BP, the optical property attracts special attention in recent years. Optical methods have been widely and successfully used in characterizing BP, not only to obtain the structural information (such as thickness and crystalline orientation), but also to probe the fundamental properties of BP in terms of the behavior of electrons, phonons, excitons etc. In this Review, a comprehensive understanding about the optical characterization of BP such as Raman, absorption, and photoluminescence is presented. Also, the unique optical properties and applications explored in recent years are reviewed.

Low-Frequency Interlayer Raman Modes to Probe Interface of Twisted Bilayer MoS2.

van der Waals homo- and heterostructures assembled by stamping monolayers together present optoelectronic properties suitable for diverse applications. Understanding the details of the interlayer stacking and resulting coupling is crucial for tuning these properties. We investigated the low-frequency interlayer shear and breathing Raman modes (<50 cm(-1)) in twisted bilayer MoS2 by Raman spectroscopy and first-principles modeling. Twisting significantly alters the interlayer stacking and coupling, leading to notable frequency and intensity changes of low-frequency modes. The frequency variation can be up to 8 cm(-1) and the intensity can vary by a factor of ∼5 for twisting angles near 0° and 60°, where the stacking is a mixture of high-symmetry stacking patterns and is thus sensitive to twisting. For twisting angles between 20° and 40°, the interlayer coupling is nearly constant because the stacking results in mismatched lattices over the entire sample. It follows that the Raman signature is relatively uniform. Note that for some samples, multiple breathing mode peaks appear, indicating nonuniform coupling across the interface. In contrast to the low-frequency interlayer modes, high-frequency intralayer Raman modes are much less sensitive to interlayer stacking and coupling. This research demonstrates the effectiveness of low-frequency Raman modes for probing the interfacial coupling and environment of twisted bilayer MoS2 and potentially other two-dimensional materials and heterostructures.

Anisotropic Electron-Photon and Electron-Phonon Interactions in Black Phosphorus.

Orthorhombic black phosphorus (BP) and other layered materials, such as gallium telluride (GaTe) and tin selenide (SnSe), stand out among two-dimensional (2D) materials owing to their anisotropic in-plane structure. This anisotropy adds a new dimension to the properties of 2D materials and stimulates the development of angle-resolved photonics and electronics. However, understanding the effect of anisotropy has remained unsatisfactory to date, as shown by a number of inconsistencies in the recent literature. We use angle-resolved absorption and Raman spectroscopies to investigate the role of anisotropy on the electron-photon and electron-phonon interactions in BP. We highlight, both experimentally and theoretically, a nontrivial dependence between anisotropy and flake thickness and photon and phonon energies. We show that once understood, the anisotropic optical absorption appears to be a reliable and simple way to identify the crystalline orientation of BP, which cannot be determined from Raman spectroscopy without the explicit consideration of excitation wavelength and flake thickness, as commonly used previously.

Ultrasmall Mode Volumes in Plasmonic Cavities of Nanoparticle-On-Mirror Structures.

The mode volume and Purcell factor are two important parameters to assess the performance of optical nanocavities. Achieving small mode volumes and high Purcell factors for nanocavity structures while simplifying their fabrication has been a major task to realize high-performance and large-scale photonic devices and systems. Different optical resonators based on nanoparticle-on-mirror (NPoM) structures are systematically analyzed, which are easy to fabricate and flexible to use. Direct comparison of these optical resonators is made through finite-difference time-domain (FDTD) simulations. The achievement of ultrasmall mode volumes below 10-7 (λ/n)3 based on the NPoM structure through FDTD simulations is demonstrated by rationally selecting the structural parameters. Such NPoM structures provide a decent Purcell factor on the order of 107 , which can effectively enhance spontaneous emission and facilitate a number of photonic applications. The simulation results are confirmed by dark field scattering and second-harmonic generation measurements. This work is scientifically important and offers practical guidelines for the design of optical resonators for state-of-the-art optical and photonic devices.

Lighting up the Raman signal of molecules in the vicinity of graphene related materials.

Surface enhanced Raman scattering (SERS) is a popular technique to detect the molecules with high selectivity and sensitivity. It has been developed for 40 years, and many reviews have been published to summarize the progress in SERS. Nevertheless, how to make the SERS signals repeatable and quantitative and how to have deeper understanding of the chemical enhancement mechanism are two big challenges. A strategy to target these issues is to develop a Raman enhancement substrate that is flat and nonmetal to replace the conventional rough and metal SERS substrate. At the same time, the newly developed substrate should have a strong interaction with the adsorbate molecules to guarantee strong chemical enhancement. The flatness of the surface allows better control of the molecular distribution and configuration, while the nonmetal surface avoids disturbance of the electromagnetic mechanism. Recently, graphene and other two-dimensional (2D) materials, which have an ideal flat surface and strong chemical interaction with plenty of organic molecules, were developed to be used as Raman enhancement substrates, which can light up the Raman signals of the molecules, and these substrates were demonstrated to be a promising for microspecies or trace species detection. This effect was named "graphene enhanced Raman scattering (GERS)". The GERS technique offers significant advantages for studying molecular vibrations due to the ultraflat and chemically inert 2D surfaces, which are newly available, especially in developing a quantitative and repeatable signal enhancement technique, complementary to SERS. Moreover, GERS is a chemical mechanism dominated effect, which offers a valuable model to study the details of the chemical mechanism. In this Account, we summarize the systematic studies exploring the character of GERS. In addition, as a practical technique, the combination of GERS with a metal substrate incorporates the advantages from both conventional SERS and GERS. The introduction of graphene to the Raman enhancement substrate extended SERS applications in a more controllable and quantitative way. Looking to the future, we expect the combination of the SERS concept with the GERS technology to lead to the solution of some important issues in chemical dynamics and in biological processes monitoring.

Molecular selectivity of graphene-enhanced Raman scattering.

Graphene-enhanced Raman scattering (GERS) is a recently discovered Raman enhancement phenomenon that uses graphene as the substrate for Raman enhancement and can produce clean and reproducible Raman signals of molecules with increased signal intensity. Compared to conventional Raman enhancement techniques, such as surface-enhanced Raman scattering (SERS) and tip-enhanced Raman scattering (TERS), in which the Raman enhancement is essentially due to the electromagnetic mechanism, GERS mainly relies on a chemical mechanism and therefore shows unique molecular selectivity. In this paper, we report graphene-enhanced Raman scattering of a variety of different molecules with different molecular properties. We report a strong molecular selectivity for the GERS effect with enhancement factors varying by as much as 2 orders of magnitude for different molecules. Selection rules are discussed with reference to two main features of the molecule, namely its molecular energy levels and molecular structures. In particular, the enhancement factor involving molecular energy levels requires the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies to be within a suitable range with respect to graphene's Fermi level, and this enhancement effect can be explained by the time-dependent perturbation theory of Raman scattering. The enhancement factor involving the choice of molecular structures indicates that molecular symmetry and substituents similar to that of the graphene structure are found to be favorable for GERS enhancement. The effectiveness of these factors can be explained by group theory and the charge-transfer interaction between molecules and graphene. Both factors, involving the molecular energy levels and structural symmetry of the molecules, suggest that a remarkable GERS enhancement requires strong molecule-graphene coupling and thus effective charge transfer between the molecules and graphene. These conclusions are further experimentally supported by the change of the UV-visible absorption spectra of molecules when in contact with graphene and these conclusions are theoretically corroborated by first-principles calculations. These research findings are important for gaining fundamental insights into the graphene-molecule interaction and the chemical mechanism in Raman enhancement, as well as for advancing the role of such understanding both in guiding chemical and molecule detection applications and in medical and biological technology developments.

Low-Frequency Interlayer Breathing Modes in Few-Layer Black Phosphorus.

As a new two-dimensional layered material, black phosphorus (BP) is a very promising material for nanoelectronics and optoelectronics. We use Raman spectroscopy and first-principles theory to characterize and understand the low-frequency (LF) interlayer breathing modes (<100 cm(-1)) in few-layer BP for the first time. Using a laser polarization dependence study and group theory analysis, the breathing modes are assigned to Ag symmetry. Compared to the high-frequency (HF) Raman modes, the LF breathing modes are considerably more sensitive to interlayer coupling and, thus, their frequencies show a stronger dependence on the number of layers. Hence, they constitute an effective means to probe both the crystalline orientation and thickness of few-layer BP. Furthermore, the temperature dependence shows that in the temperature range -150 to 30 °C, the breathing modes have a weak anharmonic behavior, in contrast to the HF Raman modes that exhibit strong anharmonicity.

Probing the interlayer coupling of twisted bilayer MoS2 using photoluminescence spectroscopy.

Two-dimensional molybdenum disulfide (MoS2) is a promising material for optoelectronic devices due to its strong photoluminescence emission. In this work, the photoluminescence of twisted bilayer MoS2 is investigated, revealing a tunability of the interlayer coupling of bilayer MoS2. It is found that the photoluminescence intensity ratio of the trion and exciton reaches its maximum value for the twisted angle 0° or 60°, while for the twisted angle 30° or 90° the situation is the opposite. This is mainly attributed to the change of the trion binding energy. The first-principles density functional theory analysis further confirms the change of the interlayer coupling with the twisted angle, which interprets our experimental results.

Dielectric screening of excitons and trions in single-layer MoS2.

Photoluminescence (PL) properties of single-layer MoS2 are indicated to have strong correlations with the surrounding dielectric environment. Blue shifts of up to 40 meV of exciton or trion PL peaks were observed as a function of the dielectric constant of the environment. These results can be explained by the dielectric screening effect of the Coulomb potential; based on this, a scaling relationship was developed with the extracted electronic band gap and exciton and trion binding energies in good agreement with theoretical estimations. It was also observed that the trion/exciton intensity ratio can be tuned by at least 1 order of magnitude with different dielectric environments. Our findings are helpful to better understand the tightly bound exciton properties in strongly quantum-confined systems and provide a simple approach to the selective and separate generation of excitons or trions with potential applications in excitonic interconnects and valleytronics.